dicom thumbs

helpers/images.py

@@ -1,6 +1,13 @@
 import base64
 import mimetypes
 
+from io import BytesIO
+
+from PIL import Image, ImageFile
+
+import pydicom
+from .pydicom_PIL import get_PIL_image
+
 def image_as_base64(image_file):
     """
     :param `image_file` for the complete path of image.
@@ -14,4 +21,37 @@ def image_as_base64(image_file):
     #    encoded_string = base64.b64encode(img_f.read())
     encoded_string = base64.b64encode(image_file.file.read())
     mimetype, enc = mimetypes.guess_type(image_file.path)
-    return "data:image/{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
+    return "data:image/{};base64,{}".format(mimetype, encoded_string.decode("utf-8"))
+
+
+
+def pil_dicom_image(source, exif_orientation=True, **options):
+    """
+    Try to open the source file directly using PIL, ignoring any errors.
+    exif_orientation
+        If EXIF orientation data is present, perform any required reorientation
+        before passing the data along the processing pipeline.
+    """
+    # Use a BytesIO wrapper because if the source is an incomplete file like
+    # object, PIL may have problems with it. For example, some image types
+    # require tell and seek methods that are not present on all storage
+    # File objects.
+    #if not source:
+    #    return
+    #source = BytesIO(source.read())
+
+    ds = pydicom.read_file("filename")
+
+    image = get_PIL_image(ds)
+
+    #with Image.open(source) as image:
+    #    # Fully load the image now to catch any problems with the image contents.
+    #    try:
+    #        ImageFile.LOAD_TRUNCATED_IMAGES = True
+    #        image.load()
+    #    finally:
+    #        ImageFile.LOAD_TRUNCATED_IMAGES = False
+
+    #if exif_orientation:
+    #    image = utils.exif_orientation(image)
+    return image

helpers/pydicom_PIL.py

@@ -0,0 +1,103 @@
+# pydicom_PIL.py
+
+"""View DICOM images using Python image Library (PIL)
+Usage:
+>>> import pydicom
+>>> from pydicom.contrib.pydicom_PIL import show_PIL
+>>> ds = pydicom.read_file("filename")
+>>> show_PIL(ds)
+Requires Numpy:
+    http://numpy.scipy.org/
+and Python Imaging Library:
+    http://www.pythonware.com/products/pil/
+"""
+# Copyright (c) 2009 Darcy Mason, Adit Panchal
+# This file is part of pydicom, relased under an MIT license.
+#    See the file LICENSE included with this distribution, also
+#    available at https://github.com/pydicom/pydicom
+
+# Based on image.py from pydicom version 0.9.3,
+#    LUT code added by Adit Panchal
+# Tested on Python 2.5.4 (32-bit) on Mac OS X 10.6
+#    using numpy 1.3.0 and PIL 1.1.7b1
+
+have_PIL = True
+try:
+    import PIL.Image
+except ImportError:
+    have_PIL = False
+
+have_numpy = True
+try:
+    import numpy as np
+except ImportError:
+    have_numpy = False
+
+
+def get_LUT_value(data, window, level):
+    """Apply the RGB Look-Up Table for the given
+       data and window/level value."""
+    if not have_numpy:
+        raise ImportError("Numpy is not available."
+                          "See http://numpy.scipy.org/"
+                          "to download and install")
+
+    return np.piecewise(data,
+                        [data <= (level - 0.5 - (window - 1) / 2),
+                         data > (level - 0.5 + (window - 1) / 2)],
+                        [0, 255, lambda data: ((data - (level - 0.5)) /
+                         (window - 1) + 0.5) * (255 - 0)])
+
+
+def get_PIL_image(dataset):
+    """Get Image object from Python Imaging Library(PIL)"""
+    if not have_PIL:
+        raise ImportError("Python Imaging Library is not available. "
+                          "See http://www.pythonware.com/products/pil/ "
+                          "to download and install")
+
+    if ('PixelData' not in dataset):
+        raise TypeError("Cannot show image -- DICOM dataset does not have "
+                        "pixel data")
+    # can only apply LUT if these window info exists
+    if ('WindowWidth' not in dataset) or ('WindowCenter' not in dataset):
+        bits = dataset.BitsAllocated
+        samples = dataset.SamplesPerPixel
+        if bits == 8 and samples == 1:
+            mode = "L"
+        elif bits == 8 and samples == 3:
+            mode = "RGB"
+        elif bits == 16:
+            # not sure about this -- PIL source says is 'experimental'
+            # and no documentation. Also, should bytes swap depending
+            # on endian of file and system??
+            mode = "I;16"
+        else:
+            raise TypeError("Don't know PIL mode for %d BitsAllocated "
+                            "and %d SamplesPerPixel" % (bits, samples))
+
+        # PIL size = (width, height)
+        size = (dataset.Columns, dataset.Rows)
+
+        # Recommended to specify all details
+        # by http://www.pythonware.com/library/pil/handbook/image.htm
+        im = PIL.Image.frombuffer(mode, size, dataset.PixelData,
+                                  "raw", mode, 0, 1)
+
+    else:
+        ew = dataset['WindowWidth']
+        ec = dataset['WindowCenter']
+        ww = int(ew.value[0] if ew.VM > 1 else ew.value)
+        wc = int(ec.value[0] if ec.VM > 1 else ec.value)
+        image = get_LUT_value(dataset.pixel_array, ww, wc)
+        # Convert mode to L since LUT has only 256 values:
+        #   http://www.pythonware.com/library/pil/handbook/image.htm
+        im = PIL.Image.fromarray(image).convert('L')
+
+    return im
+
+
+def show_PIL(dataset):
+    """Display an image using the Python Imaging Library (PIL)"""
+    im = get_PIL_image(dataset)
+    im.show()

rad/settings.py

@@ -198,7 +198,9 @@ THUMBNAIL_ALIASES = {
     },
 }
 
+THUMBNAIL_SOURCE_GENERATORS = ('easy_thumbnails.source_generators.pil_image', 'helpers.images.pil_dicom_image')
+
 try:
     from .settings_local import *
 except ImportError:
-    pass
+    pass

requirements.txt

@@ -13,4 +13,5 @@ django-filer
 psycopg2-binary
 django-sortedm2m
 pytesseract
-opencv-python
+opencv-python
+pydicom