Ross
113 lines
3.2 KiB
Python
113 lines
3.2 KiB
Python
import base64
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import mimetypes
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from io import BytesIO
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from PIL import Image, ImageFile
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import pydicom
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import sys
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import glob
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try:
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from .pydicom_PIL import get_PIL_image
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except:
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from pydicom_PIL import get_PIL_image
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def image_as_base64(image_file):
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"""
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:param `image_file` for the complete path of image.
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:param `format` is format for image, eg: `png` or `jpg`.
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"""
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# if not os.path.isfile(image_file):
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# return None
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encoded_string = ""
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# with open(image_file, 'rb') as img_f:
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# encoded_string = base64.b64encode(img_f.read())
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encoded_string = base64.b64encode(image_file.file.read())
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mimetype, enc = mimetypes.guess_type(image_file.path)
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# Treat unknown files as dicom
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if None == mimetype:
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return "data:application/dicom;base64,{}".format(encoded_string.decode("utf-8"))
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if "dicom" in mimetype or "octet-stream" in mimetype:
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return "data:{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
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return "data:image/{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
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def pil_dicom_image(source, exif_orientation=True, **options):
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"""
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Try to open the source file directly using PIL, ignoring any errors.
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exif_orientation
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If EXIF orientation data is present, perform any required reorientation
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before passing the data along the processing pipeline.
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"""
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# Use a BytesIO wrapper because if the source is an incomplete file like
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# object, PIL may have problems with it. For example, some image types
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# require tell and seek methods that are not present on all storage
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# File objects.
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#if not source:
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# return
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#source = BytesIO(source.read())
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# open file with pydicom
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ds = pydicom.read_file(source)
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# return the image file
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return get_PIL_image(ds)
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#with Image.open(source) as image:
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# # Fully load the image now to catch any problems with the image contents.
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# try:
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# ImageFile.LOAD_TRUNCATED_IMAGES = True
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# image.load()
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# finally:
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# ImageFile.LOAD_TRUNCATED_IMAGES = False
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#if exif_orientation:
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# image = utils.exif_orientation(image)
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def show_PIL(dataset):
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"""Display an image using the Python Imaging Library (PIL)"""
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im = get_PIL_image(dataset)
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im.show()
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def get_dicom_order(path):
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# load the DICOM files
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files = []
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for fname in glob.glob(path, recursive=False):
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print("loading: {}".format(fname))
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files.append((fname, pydicom.dcmread(fname)))
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print("file count: {}".format(len(files)))
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# skip files with no SliceLocation (eg scout views)
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slices = []
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map = {}
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skipcount = 0
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for fname, f in files:
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print(dir(f))
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print(fname)
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if hasattr(f, 'SliceLocation'):
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slices.append(f)
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map[f.SliceLocation] = fname
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else:
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skipcount = skipcount + 1
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print("skipped, no SliceLocation: {}".format(skipcount))
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# ensure they are in the correct order
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slices = sorted(slices, key=lambda s: s.SliceLocation)
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#print(slices)
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for i in slices:
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print(map[i.SliceLocation])
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get_dicom_order("/home/ross/Downloads/DICOM HEAD/STD4/SER1/*.dcm") |