RawImageReading/RawImageReading.py

#!/usr/bin/env python
# =========================================================================
#
#  Copyright NumFOCUS
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0.txt
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
# =========================================================================
 
import argparse
import os
import tempfile
 
import SimpleITK as sitk
 
 
def read_raw(
    binary_file_name,
    image_size,
    sitk_pixel_type,
    image_spacing=None,
    image_origin=None,
    big_endian=False,
):
    """
    Read a raw binary scalar image.
 
    Parameters
    ----------
    binary_file_name (str): Raw, binary image file content.
    image_size (tuple like): Size of image (e.g. [2048,2048])
    sitk_pixel_type (SimpleITK pixel type: Pixel type of data (e.g.
        sitk.sitkUInt16).
    image_spacing (tuple like): Optional image spacing, if none given assumed
        to be [1]*dim.
    image_origin (tuple like): Optional image origin, if none given assumed to
        be [0]*dim.
    big_endian (bool): Optional byte order indicator, if True big endian, else
        little endian.
 
    Returns
    -------
    SimpleITK image or None if fails.
    """
 
    pixel_dict = {
        sitk.sitkUInt8: "MET_UCHAR",
        sitk.sitkInt8: "MET_CHAR",
        sitk.sitkUInt16: "MET_USHORT",
        sitk.sitkInt16: "MET_SHORT",
        sitk.sitkUInt32: "MET_UINT",
        sitk.sitkInt32: "MET_INT",
        sitk.sitkUInt64: "MET_ULONG_LONG",
        sitk.sitkInt64: "MET_LONG_LONG",
        sitk.sitkFloat32: "MET_FLOAT",
        sitk.sitkFloat64: "MET_DOUBLE",
    }
    direction_cosine = [
        "1 0 0 1",
        "1 0 0 0 1 0 0 0 1",
        "1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1",
    ]
    dim = len(image_size)
    header = [
        "ObjectType = Image\n".encode(),
        (f"NDims = {dim}\n").encode(),
        ("DimSize = " + " ".join([str(v) for v in image_size]) + "\n").encode(),
        (
            "ElementSpacing = "
            + (
                " ".join([str(v) for v in image_spacing])
                if image_spacing
                else " ".join(["1"] * dim)
            )
            + "\n"
        ).encode(),
        (
            "Offset = "
            + (
                " ".join([str(v) for v in image_origin])
                if image_origin
                else " ".join(["0"] * dim) + "\n"
            )
        ).encode(),
        ("TransformMatrix = " + direction_cosine[dim - 2] + "\n").encode(),
        ("ElementType = " + pixel_dict[sitk_pixel_type] + "\n").encode(),
        "BinaryData = True\n".encode(),
        ("BinaryDataByteOrderMSB = " + str(big_endian) + "\n").encode(),
        # ElementDataFile must be the last entry in the header
        ("ElementDataFile = " + os.path.abspath(binary_file_name) + "\n").encode(),
    ]
    fp = tempfile.NamedTemporaryFile(suffix=".mhd", delete=False)
 
    print(header)
 
    # Not using the tempfile with a context manager and auto-delete
    # because on windows we can't open the file a second time for ReadImage.
    fp.writelines(header)
    fp.close()
    img = sitk.ReadImage(fp.name)
    os.remove(fp.name)
    return img
 
 
parser = argparse.ArgumentParser()
parser.add_argument("raw_file_name", help="path to raw binary image file")
parser.add_argument(
    "out_file_name", help="output file name when image read as little endian"
)
parser.add_argument(
    "big_endian",
    type=lambda v: v.lower() in {"1", "true"},
    help="'false' for little ending or 'true'for big " "endian",
)
parser.add_argument(
    "sitk_pixel_type", help="SimpleITK pixel type (e.g. sitk.sitkUInt16)"
)
parser.add_argument("sz", nargs="+", help="image size, x,y,...", type=int)
args = parser.parse_args()
 
string_to_pixelType = {
    "sitkUInt8": sitk.sitkUInt8,
    "sitkInt8": sitk.sitkInt8,
    "sitkUInt16": sitk.sitkUInt16,
    "sitkInt16": sitk.sitkInt16,
    "sitkUInt32": sitk.sitkUInt32,
    "sitkInt32": sitk.sitkInt32,
    "sitkUInt64": sitk.sitkUInt64,
    "sitkInt64": sitk.sitkInt64,
    "sitkFloat32": sitk.sitkFloat32,
    "sitkFloat64": sitk.sitkFloat64,
}
 
# Read the image using both big and little endian
image = read_raw(
    binary_file_name=args.raw_file_name,
    image_size=args.sz,
    sitk_pixel_type=string_to_pixelType[args.sitk_pixel_type],
    big_endian=args.big_endian,
)
 
sitk.WriteImage(image, args.out_file_name)
 
if "SITK_NOSHOW" not in os.environ:
    sitk.Show(image, "raw converted")