WIP

Author: scaramallion

Cargo.lock

@@ -12,3 +12,4 @@ crate-type = ["cdylib"]
 
 [dependencies]
 pyo3 = { version = "0.24.2", features = ["extension-module"] }
+bitvec = { version = "1.0.1" }

Cargo.toml

@@ -8,7 +8,7 @@
 
 ## pylibjpeg-rle
 
-A fast DICOM ([PackBits](https://en.wikipedia.org/wiki/PackBits)) RLE plugin for [pylibjpeg](https://github.com/pydicom/pylibjpeg), written in Rust with a Python 3.7+ wrapper.
+A fast DICOM ([PackBits](https://en.wikipedia.org/wiki/PackBits)) RLE plugin for [pylibjpeg](https://github.com/pydicom/pylibjpeg), written in Rust with a Python wrapper.
 
 Linux, MacOS and Windows are all supported.
 
@@ -85,32 +85,32 @@ ds.save_as('as_rle.dcm')
 ### Benchmarks
 #### Decoding
 
-Time per 1000 decodes, pydicom's default RLE handler vs. pylibjpeg-rle
+Time per 1000 decodes, pydicom's default RLE decoder vs. pylibjpeg-rle:
 
 | Dataset                     | Pixels  | Bytes   | pydicom | pylibjpeg-rle |
 | ---                         | ---     | ---     | ---     | ---           |
-| OBXXXX1A_rle.dcm            | 480,000 | 480,000 | 4.89 s  |        0.79 s |
-| OBXXXX1A_rle_2frame.dcm     | 960,000 | 960,000 | 9.89 s  |        1.65 s |
-| SC_rgb_rle.dcm              |  10,000 |  30,000 | 0.20 s  |        0.15 s |
-| SC_rgb_rle_2frame.dcm       |  20,000 |  60,000 | 0.32 s  |        0.18 s |
-| MR_small_RLE.dcm            |   4,096 |   8,192 | 0.35 s  |        0.13 s |
-| emri_small_RLE.dcm          |  40,960 |  81,920 | 1.13 s  |        0.28 s |
-| SC_rgb_rle_16bit.dcm        |  10,000 |  60,000 | 0.33 s  |        0.17 s |
-| SC_rgb_rle_16bit_2frame.dcm |  20,000 | 120,000 | 0.56 s  |        0.21 s |
-| rtdose_rle_1frame.dcm       |     100 |     400 | 0.12 s  |        0.13 s |
-| rtdose_rle.dcm              |   1,500 |   6,000 | 0.53 s  |        0.26 s |
-| SC_rgb_rle_32bit.dcm        |  10,000 | 120,000 | 0.56 s  |        0.19 s |
-| SC_rgb_rle_32bit_2frame.dcm |  20,000 | 240,000 | 1.03 s  |        0.28 s |
+| OBXXXX1A_rle.dcm            | 480,000 | 480,000 |  5.7 s  |        1.1 s  |
+| OBXXXX1A_rle_2frame.dcm     | 960,000 | 960,000 | 11.5 s  |        2.1 s  |
+| SC_rgb_rle.dcm              |  10,000 |  30,000 | 0.28 s  |        0.19 s |
+| SC_rgb_rle_2frame.dcm       |  20,000 |  60,000 | 0.45 s  |        0.28 s |
+| MR_small_RLE.dcm            |   4,096 |   8,192 | 0.46 s  |        0.15 s |
+| emri_small_RLE.dcm          |  40,960 |  81,920 | 1.8 s   |        0.67 s |
+| SC_rgb_rle_16bit.dcm        |  10,000 |  60,000 | 0.48 s  |        0.25 s |
+| SC_rgb_rle_16bit_2frame.dcm |  20,000 | 120,000 | 0.86 s  |        0.39 s |
+| rtdose_rle_1frame.dcm       |     100 |     400 | 0.16 s  |        0.13 s |
+| rtdose_rle.dcm              |   1,500 |   6,000 | 1.0 s   |        0.64 s |
+| SC_rgb_rle_32bit.dcm        |  10,000 | 120,000 | 0.82 s  |        0.35 s |
+| SC_rgb_rle_32bit_2frame.dcm |  20,000 | 240,000 | 1.5 s   |        0.60 s |
 
 #### Encoding
 
-Time per 1000 encodes, pydicom's default RLE handler vs. pylibjpeg-rle
+Time per 1000 encodes, pydicom's default RLE encoder vs. pylibjpeg-rle and [python-gdcm](https://github.com/tfmoraes/python-gdcm):
 
-| Dataset            | Pixels  | Bytes   | pydicom | pylibjpeg-rle |
-| ---                | ---     | ---     | ---     | ---           |
-| OBXXXX1A.dcm       | 480,000 | 480,000 | 30.7 s  |       1.36 s  |
-| SC_rgb.dcm         |  10,000 |  30,000 | 1.80 s  |       0.09 s  |
-| MR_small.dcm       |   4,096 |   8,192 | 2.29 s  |       0.04 s  |
-| SC_rgb_16bit.dcm   |  10,000 |  60,000 | 3.57 s  |       0.17 s  |
-| rtdose_1frame.dcm  |     100 |     400 | 0.19 s  |       0.003 s |
-| SC_rgb_32bit.dcm   |  10,000 | 120,000 | 7.20 s  |       0.33 s  |
+| Dataset            | Pixels  | Bytes   | pydicom | pylibjpeg-rle | python-gdcm |
+| ---                | ---     | ---     | ---     | ---           | ---         |
+| OBXXXX1A.dcm       | 480,000 | 480,000 | 30.6 s  |       1.4 s   | 1.5 s       |
+| SC_rgb.dcm         |  10,000 |  30,000 |  1.9 s  |       0.11 s  | 0.21 s      |
+| MR_small.dcm       |   4,096 |   8,192 |  3.0 s  |       0.11 s  | 0.29 s      |
+| SC_rgb_16bit.dcm   |  10,000 |  60,000 |  3.6 s  |       0.18 s  | 0.28 s      |
+| rtdose_1frame.dcm  |     100 |     400 | 0.28 s  |       0.04 s  | 0.14 s      |
+| SC_rgb_32bit.dcm   |  10,000 | 120,000 |  7.1 s  |       0.32 s  | 0.43 s      |

README.md

@@ -32,7 +32,7 @@ keywords = ["dicom pydicom python rle pylibjpeg rust"]
 license = "MIT"
 name = "pylibjpeg-rle"
 readme = "README.md"
-version = "2.1.0"
+version = "2.2.0.dev0"
 requires-python = ">=3.10"
 dependencies = [
   "numpy>=2.0",

pyproject.toml

@@ -106,6 +106,10 @@ def encode_array(
 
     .. versionadded:: 1.1
 
+    .. versionchanged:: 2.2
+
+        Added support for 'bits_allocated' 1.
+
     Parameters
     ----------
     arr : numpy.ndarray
@@ -124,7 +128,7 @@ def encode_array(
         * ``samples_per_px': int`` the number of samples per pixel, either
           1 for monochrome or 3 for RGB or similar data.
         * ``'bits_per_px': int`` the number of bits needed to contain each
-          pixel, either 8, 16, 32 or 64.
+          pixel, either 1, 8, 16, 32 or 64.
         * ``'nr_frames': int`` the number of frames in `arr`, required if
           more than one frame is present.
 
@@ -169,6 +173,10 @@ def encode_pixel_data(
         to 15 in order to meet the requirements of the *RLE Lossless*
         transfer syntax.
 
+    .. versionchanged:: 2.2
+
+        Added support for 'bits_allocated' 1.
+
     Parameters
     ----------
     src : bytes
@@ -189,7 +197,7 @@ def encode_pixel_data(
         * ``samples_per_pixel': int`` the number of samples per pixel, either
           1 for monochrome or 3 for RGB or similar data.
         * ``'bits_allocated': int`` the number of bits needed to contain each
-          pixel, either 8, 16, 32 or 64.
+          pixel, either 1, 8, 16, 32 or 64.
 
     Returns
     -------
@@ -212,9 +220,9 @@ def encode_pixel_data(
         msg = "(0028,0002) 'Samples per Pixel'" if ds else "'samples_per_pixel'"
         raise ValueError(f"{msg} must be 1 or 3")
 
-    if bpp not in [8, 16, 32, 64]:
+    if bpp not in [1, 8, 16, 32, 64]:
         msg = "(0028,0100) 'Bits Allocated'" if ds else "'bits_allocated'"
-        raise ValueError(f"{msg} must be 8, 16, 32 or 64")
+        raise ValueError(f"{msg} must be 1, 8, 16, 32 or 64")
 
     if bpp / 8 * spp > 15:
         raise ValueError(
@@ -235,6 +243,7 @@ def encode_pixel_data(
     return cast(bytes, encode_frame(src, r, c, spp, bpp, byteorder))
 
 
+# TODO: unpack Bits Stored 1
 def generate_frames(ds: "Dataset", reshape: bool = True) -> Iterator[np.ndarray]:
     """Yield a *Pixel Data* frame from `ds` as an :class:`~numpy.ndarray`.
 
@@ -310,6 +319,7 @@ def generate_frames(ds: "Dataset", reshape: bool = True) -> Iterator[np.ndarray]
             yield arr.transpose(1, 2, 0)
 
 
+# TODO: unpack Bits Stored 1
 def pixel_array(ds: "Dataset") -> "np.ndarray":
     """Return the entire *Pixel Data* as an :class:`~numpy.ndarray`.