Esempio n. 1
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	def test_dicom_class_validate(self):
		mu = mudicom.load(self.fnames[0])
		dcm = mu.validate()
		self.assertEqual(len(dcm['errors']), 6)
		self.assertEqual(len(dcm['warnings']), 18)

		mu = mudicom.load(self.fnames[1])
		dcm = mu.validate()
		self.assertEqual(len(dcm['errors']), 7)
		self.assertEqual(len(dcm['warnings']), 18)
Esempio n. 2
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    def test_dicom_class_validate(self):
        mu = mudicom.load(self.fnames[0])
        dcm = mu.validate()
        self.assertEqual(len(dcm['errors']), 6)
        self.assertEqual(len(dcm['warnings']), 18)

        mu = mudicom.load(self.fnames[1])
        dcm = mu.validate()
        self.assertEqual(len(dcm['errors']), 7)
        self.assertEqual(len(dcm['warnings']), 18)
Esempio n. 3
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 def test_get_numpy(self):
     for fname in self.fnames:
         mu = mudicom.load(fname)
         img = mu.image
         gnp = img.numpy
         self.assertIsInstance(gnp, numpy.ndarray)
         self.assertEqual(gnp.dtype, numpy.float)
Esempio n. 4
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 def test_get_numpy(self):
     for fname in self.fnames:
         mu = mudicom.load(fname)
         img = mu.image
         gnp = img.numpy
         self.assertIsInstance(gnp, numpy.ndarray)
         self.assertEqual(gnp.dtype, numpy.float)
Esempio n. 5
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 def test_get_element(self):
     for fname in self.fnames:
         mu = mudicom.load(fname)
         #reader = mu.read()
         self.assertIsInstance(mu.find(0x004, 0x1220), list)
         self.assertIsInstance(mu.find(name="Modality"), list)
         self.assertIsInstance(mu.find(VR="PN"), list)
Esempio n. 6
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    def test_walk_dataset(self):
        for fname in self.fnames:
            mu = mudicom.load(fname)
            #reader = mu.read()

            tags = list(mu.walk(lambda ds: ds.GetTag()))
            self.assertIsInstance(tags, list)
            self.assertIsNot(len(tags), 0)
            for tag in tags:
                self.assertIsInstance(tag, gdcm.Tag)

            tags = list(mu.walk(lambda ds: None))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertEqual(tag, None)

            tags = list(mu.walk(lambda ds: False))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertFalse(tag)

            tags = list(mu.walk(lambda ds: True))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertTrue(tag)
Esempio n. 7
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    def test_walk_dataset(self):
        for fname in self.fnames:
            mu = mudicom.load(fname)
            #reader = mu.read()

            tags = list(mu.walk(lambda ds: ds.GetTag()))
            self.assertIsInstance(tags, list)
            self.assertIsNot(len(tags), 0)
            for tag in tags:
                self.assertIsInstance(tag, gdcm.Tag)

            tags = list(mu.walk(lambda ds: None))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertEqual(tag, None)

            tags = list(mu.walk(lambda ds: False))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertFalse(tag)

            tags = list(mu.walk(lambda ds: True))
            self.assertIsInstance(tags, list)
            for tag in tags:
                self.assertTrue(tag)
Esempio n. 8
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 def test_get_element(self):
     for fname in self.fnames:
         mu = mudicom.load(fname)
         #reader = mu.read()
         self.assertIsInstance(mu.find(0x004, 0x1220), list)
         self.assertIsInstance(mu.find(name="Modality"), list)
         self.assertIsInstance(mu.find(VR="PN"), list)
Esempio n. 9
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def dcm2thumbnail(source_path, target_path, resize_row=128, resize_col=128):
    # define output
    dict_return = {}
    dict_return['status'] = 1
    dict_return['paths'] = target_path
    filename = source_path.split(os.path.sep)[-1]
    if filename.split('.')[-1] == 'dcm':
        filename = filename[0:len(filename) - 4]
    if target_path[-1] != os.path.sep:
        target_path += os.path.sep

    # get usefull dicom information
    try:
        dcm_head = dicom.read_file(source_path)
    except IOError:
        dict_return['status'] = 0
        print('read dicom error')
        return dict_return
    rescale_intercept = dcm_head.RescaleIntercept
    rescale_slope = dcm_head.RescaleSlope

    # get original pixel
    try:
        mud = mudicom.load(source_path)
    except mudicom.exceptions.InvalidDicom:
        dict_return['status'] = 0
        print('read mudicom error')
        return dict_return
    pixel_ori = (mud.image).numpy
    pixel_ori = pixel_ori.astype(np.int16)

    # pixel to HU value
    pixel_hu = copy.deepcopy(pixel_ori)
    pixel_hu = (rescale_slope * pixel_hu.astype(np.float64)).astype(np.int16)
    pixel_hu += np.int16(rescale_intercept)
    pixel_hu = np.array(pixel_hu, dtype=np.int16)

    # adjust window
    default_img = adjust_window(pixel_hu, *(40, 400))
    default_img = scipy.misc.imresize(default_img, (resize_row, resize_col),
                                      'nearest')

    # return status
    try:
        scipy.misc.imsave(target_path + filename + '.jpg', default_img)
    except IOError:
        dict_return['status'] = 0
        return dict_return
    dict_return['paths'] = target_path + filename + '.jpg'

    return dict_return
Esempio n. 10
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    def test_get_dataset(self):
        for fname in self.fnames:
            mu = mudicom.load(fname)
            ds = mu.read()
            self.assertIsInstance(ds, list)
            self.assertIsNot(len(ds), 0)

            for element in ds:
                self.assertTrue(hasattr(element, "name"))
                self.assertTrue(hasattr(element, "value"))
                self.assertTrue(hasattr(element, "VR"))
                self.assertTrue(hasattr(element, "VL"))
                self.assertTrue(hasattr(element, "tag"))
                self.assertTrue("group" in element.tag)
                self.assertTrue("element" in element.tag)
                self.assertTrue("str" in element.tag)
Esempio n. 11
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    def test_get_dataset(self):
        for fname in self.fnames:
            mu = mudicom.load(fname)
            ds = mu.read()
            self.assertIsInstance(ds, list)
            self.assertIsNot(len(ds), 0)

            for element in ds:
                self.assertTrue(hasattr(element, "name"))
                self.assertTrue(hasattr(element, "value"))
                self.assertTrue(hasattr(element, "VR"))
                self.assertTrue(hasattr(element, "VL"))
                self.assertTrue(hasattr(element, "tag"))
                self.assertTrue("group" in element.tag)
                self.assertTrue("element" in element.tag)
                self.assertTrue("str" in element.tag)
Esempio n. 12
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    def GetPixelByTransferSyntax(self):
        if self.ts == uid.ImplicitVRLittleEndian or self.ts == uid.JPEGLossless:
            self.ds.decompress()
            self.pixel = self.ds.pixel_array

        elif self.ts == uid.ExplicitVRLittleEndian or self.ts == uid.JPEG2000Lossy:
            import mudicom
            mu = mudicom.load(self.fPath)
            # returns array of data elements as dicts
            mu.read()
            # creates image object
            img = mu.image  # before v0.1.0 this was mu.image()
            # returns numpy array
            self.pixel = img.numpy  # before v0.1.0 this was mu.numpy()fileFolder
        else:
            print self.ts + " can not support Transfer Syntax"
            return

        return self.pixel
Esempio n. 13
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    q[1] = max(q[1],1)  
    tf=[[0,0,0,0,0],[q[0],0,0,0,0],[q[1],1,1,1,0.5],[data.max(),1,1,1,1]]  
      
    actor_list = volumeRender(data, tf=tf, spacing=img.GetSpacing())  
      
    vtk_basic(actor_list)  

下面一个不错的软件:

https://github.com/bastula/dicompyler
还有一个python的库mudicom,https://github.com/neurosnap/mudicom

[python] view plain copy

    import mudicom  
    mu = mudicom.load("mudicom/tests/dicoms/ex1.dcm")  
      
    # returns array of data elements as dicts  
    mu.read()  
      
    # returns dict of errors and warnings for DICOM  
    mu.validate()  
      
    # basic anonymization  
    mu.anonymize()  
    # save anonymization  
    mu.save_as("dicom.dcm")  
      
    # creates image object  
    img = mu.image # before v0.1.0 this was mu.image()  
    # returns numpy array  
Esempio n. 14
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File: run.py Progetto: kfrankc/cs188
# import cv2
import numpy as np
from matplotlib import pyplot as plt
# from PIL import Image

from skimage.color import rgb2gray
from skimage.filters import threshold_mean
from skimage import util
from skimage.filters import median
from skimage.morphology import disk, skeletonize, binary_dilation, binary_erosion, binary_closing

# from skimage.exposure import equalize_adapthist

# ds = dicom.read_file("2d_angiogram_2.dcm")
img_id = 1
mu = mudicom.load("2d_angiogram_" + str(img_id) + ".dcm")
mu_out = mu.image
pixel_array = mu_out.numpy

# with open("pixel_array", "w") as f:
# 	np.save(f, pixel_array)
# exit()

i = 1

# fig2, ax = plt.subplots(2, 2, figsize=(10, 8))

fig = plt.figure(frameon=False)
ax = plt.Axes(fig, [0., 0., 1., 1.])
fig.set_size_inches(5.12, 5.12)
ax.set_axis_off()
Esempio n. 15
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    if event.key == 'j':
        previous_slice(ax)
    elif event.key == 'k':
        next_slice(ax)
    fig.canvas.draw()


def previous_slice(ax):
    volume = ax.volume
    ax.index = (ax.index - 1) % volume.shape[0]  # wrap around using %
    ax.images[0].set_array(volume[ax.index])


def next_slice(ax):
    volume = ax.volume
    ax.index = (ax.index + 1) % volume.shape[0]
    ax.images[0].set_array(volume[ax.index])


fpath = "/home/j_69/Fiducial Localization - MRI Scans/pvc/Sequential Scan/DICOM/PA1/ST1/SE2"  ## edit this accordingly
slices = 176  ## edit this accordingly

mu = []
arry = []
for i in range(1, slices):
    mu.append(dicom.load(fpath + "/IM" + str(i)))
    arry.append(mu[i - 1].image.numpy)

multi_slice_viewer(np.array(arry))
plt.show()
Esempio n. 16
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view_pointcloud(surfaceVoxels_ref, color='y')
plt.show()

##multi_slice_viewer(voxel_ndarray_ref)
##plt.show()

### Using Rawfloating image, as patient data missing for this view

directory_flo1 = "/home/j_69/Fiducial Localization - MRI Scans/glass/Glass Scan Coronal 0.9 mm/DICOM/PA1/ST1/SE2"  ## edit this accordingly
slices = 256  ## edit this accordingly

mu = []
arry = []
for i in range(1, slices):
    mu.append(mudicom.load(directory_flo1 + "/IM" + str(i)))
    arry.append(mu[i - 1].image.numpy)
voxel_ndarray_flo1 = np.array(arry)

surfaceVoxels_flo1 = getSurfaceVoxels(voxel_ndarray_flo1)
print surfaceVoxels_flo1

view_pointcloud(surfaceVoxels_ref, color='b')
plt.show()

print("Applying ICP...")

ijkmat = icp(surfaceVoxels_ref, surfaceVoxels_flo1, max_iterations=40)
print(ijkmat)
"""
voxel_ndarray_flo1 = snd.rotate(voxel_ndarray_ref,15)
Esempio n. 17
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 def test_animation_numpy_shape(self):
     mu = mudicom.load(self.fnames[2])
     image = mu.image
     self.assertEqual(len(image.numpy.shape), 3)
     self.assertEqual(image.numpy.shape[0], 76)
Esempio n. 18
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 def test_animation_numpy_shape(self):
     mu = mudicom.load(self.fnames[2])
     image = mu.image
     self.assertEqual(len(image.numpy.shape), 3)
     self.assertEqual(image.numpy.shape[0], 76)
Esempio n. 19
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 def _generate_data_elements(self, filename):
     mu = mudicom.load(uploaded_dicoms.path(filename))
     return [DicomDataElement(e) for e in mu.find()]