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Pydicom tutorial





In [1]:



    


import scipy
import scipy.misc
# import skimage
# import skimage.io
import numpy as np
# import urllib
# import cStringIO

import matplotlib.pyplot as plt



    











In [2]:



    


# conda install -c conda-forge -c mjirik scikit-image



    











In [3]:



    


import pydicom
import os.path
import glob

if 5 < 10:
    print("ahoj " + str(18))
    print(10)
else:
    print("je to mensi")


pth = os.path.expanduser("~/data/medical/orig/jatra_5mm/*.dcm")



    


















    






ahoj18
10

















In [4]:



    


pth



    


















    
Out[4]:








'C:\\Users\\miros/data/medical/orig/jatra_5mm/*.dcm'

















In [5]:



    


pths = glob.glob(pth)
pths



    


















    
Out[5]:








['C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0001.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0002.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0003.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0004.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0005.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0006.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0007.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0008.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0009.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0010.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0011.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0012.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0013.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0014.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0015.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0016.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0017.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0018.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0019.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0020.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0021.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0022.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0023.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0024.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0025.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0026.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0027.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0028.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0029.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0030.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0031.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0032.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0033.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0034.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0035.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0036.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0037.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0038.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0039.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0040.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0041.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0042.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0043.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0044.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0045.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0046.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0047.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0048.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0049.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0050.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0051.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0052.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0053.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0054.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0055.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0056.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0057.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0058.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0059.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0060.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0061.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0062.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0063.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0064.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0065.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0066.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0067.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0068.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0069.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0070.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0071.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0072.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0073.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0074.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0075.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0076.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0077.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0078.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0079.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0080.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0081.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0082.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0083.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0084.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0085.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0086.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0087.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0088.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0089.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0090.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0091.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0092.dcm',
 'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0093.dcm']

















In [6]:



    


pths[0]



    


















    
Out[6]:








'C:\\Users\\miros/data/medical/orig/jatra_5mm\\IM-0001-0001.dcm'

















In [7]:



    


dcmobj = pydicom.read_file(pths[0])
# dcmobj

Dicom tags





In [8]:



    


dir(dcmobj)



    


















    
Out[8]:








['AccessionNumber',
 'AcquisitionDate',
 'AcquisitionNumber',
 'AcquisitionTime',
 'BitsAllocated',
 'BitsStored',
 'BodyPartExamined',
 'CTDIvol',
 'Columns',
 'ContentDate',
 'ContentTime',
 'ContrastBolusAgent',
 'ContrastBolusIngredientConcentration',
 'ContrastBolusVolume',
 'ContrastFlowDuration',
 'ContrastFlowRate',
 'ConvolutionKernel',
 'DataCollectionDiameter',
 'DateOfLastCalibration',
 'DerivationDescription',
 'DeviceSerialNumber',
 'DistanceSourceToDetector',
 'DistanceSourceToPatient',
 'EstimatedDoseSaving',
 'ExposureModulationType',
 'FrameOfReferenceUID',
 'GantryDetectorTilt',
 'HighBit',
 'ImageComments',
 'ImageFrameOrigin',
 'ImageOrientationPatient',
 'ImagePositionPatient',
 'ImageType',
 'InstanceNumber',
 'KVP',
 'LargestImagePixelValue',
 'Manufacturer',
 'ManufacturerModelName',
 'Modality',
 'NumberOfFramesInOverlay',
 'OverlayBitPosition',
 'OverlayBitsAllocated',
 'OverlayColumns',
 'OverlayData',
 'OverlayDescription',
 'OverlayOrigin',
 'OverlayRows',
 'OverlayType',
 'PatientAddress',
 'PatientAge',
 'PatientBirthDate',
 'PatientID',
 'PatientName',
 'PatientPosition',
 'PatientSex',
 'PerformedStationAETitle',
 'PerformingPhysicianName',
 'PhotometricInterpretation',
 'PixelData',
 'PixelRepresentation',
 'PixelSpacing',
 'PositionReferenceIndicator',
 'ProcedureCodeSequence',
 'ProtocolName',
 'ReconstructionDiameter',
 'ReferencedImageSequence',
 'ReferringPhysicianName',
 'RequestAttributesSequence',
 'RequestedProcedureCodeSequence',
 'RequestedProcedureDescription',
 'RescaleIntercept',
 'RescaleSlope',
 'RotationDirection',
 'Rows',
 'SOPClassUID',
 'SOPInstanceUID',
 'SamplesPerPixel',
 'SeriesDate',
 'SeriesDescription',
 'SeriesInstanceUID',
 'SeriesNumber',
 'SeriesTime',
 'SingleCollimationWidth',
 'SliceLocation',
 'SliceThickness',
 'SmallestImagePixelValue',
 'SoftwareVersions',
 'SourceImageSequence',
 'SpecificCharacterSet',
 'SpiralPitchFactor',
 'StationName',
 'StorageMediaFileSetUID',
 'StudyDate',
 'StudyDescription',
 'StudyID',
 'StudyInstanceUID',
 'StudyTime',
 'TableFeedPerRotation',
 'TableHeight',
 'TableSpeed',
 'TimeOfLastCalibration',
 'TotalCollimationWidth',
 'WindowCenter',
 'WindowCenterWidthExplanation',
 'WindowWidth',
 '__contains__',
 '__delattr__',
 '__delitem__',
 '__dir__',
 '__enter__',
 '__eq__',
 '__exit__',
 '__format__',
 '__ge__',
 '__getattr__',
 '__getattribute__',
 '__getitem__',
 '__gt__',
 '__init__',
 '__init_subclass__',
 '__iter__',
 '__le__',
 '__len__',
 '__lt__',
 '__ne__',
 '__new__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__setitem__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 '__weakref__',
 '_character_set',
 '_convert_YBR_to_RGB',
 '_get_pixel_array',
 '_is_uncompressed_transfer_syntax',
 '_pretty_str',
 '_reshape_pixel_array',
 '_slice_dataset',
 'add',
 'add_new',
 'clear',
 'convert_pixel_data',
 'copy',
 'data_element',
 'decode',
 'decompress',
 'dir',
 'formatted_lines',
 'fromkeys',
 'get',
 'get_item',
 'group_dataset',
 'items',
 'iterall',
 'keys',
 'pixel_array',
 'pop',
 'popitem',
 'remove_private_tags',
 'save_as',
 'setdefault',
 'top',
 'trait_names',
 'update',
 'values',
 'walk']

















In [9]:



    


dcmobj.SeriesDescription



    


















    
Out[9]:








'DE_Abdom_1F  5.0  B30f M_0.3'

















In [10]:



    


hasattr(dcmobj, "SeriesDescription")



    


















    
Out[10]:








True

Obrazová data





In [11]:



    


data3d = dcmobj.pixel_array
data3d



    


















    
Out[11]:








array([[0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       ..., 
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0]], dtype=uint16)

















In [12]:



    


plt.imshow(data3d[:, :])
plt.colorbar()



    


















    
Out[12]:








<matplotlib.colorbar.Colorbar at 0x1ec4ba80240>










    
























In [13]:



    


plt.imshow(data3d[:, :], cmap="gray")



    


















    
Out[13]:








<matplotlib.image.AxesImage at 0x1ec4bd91588>

Processing files in directory

$a^2 + 3 = y$





In [14]:



    


for filename in pths:
    dcmobj = pydicom.read_file(filename)
    print(dcmobj.SliceLocation, filename)



    


















    






-601.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0001.dcm
-606.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0002.dcm
-611.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0003.dcm
-616.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0004.dcm
-621.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0005.dcm
-626.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0006.dcm
-631.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0007.dcm
-636.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0008.dcm
-641.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0009.dcm
-646.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0010.dcm
-651.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0011.dcm
-656.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0012.dcm
-661.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0013.dcm
-666.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0014.dcm
-671.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0015.dcm
-676.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0016.dcm
-681.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0017.dcm
-686.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0018.dcm
-691.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0019.dcm
-696.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0020.dcm
-701.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0021.dcm
-706.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0022.dcm
-711.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0023.dcm
-716.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0024.dcm
-721.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0025.dcm
-726.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0026.dcm
-731.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0027.dcm
-736.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0028.dcm
-741.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0029.dcm
-746.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0030.dcm
-751.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0031.dcm
-756.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0032.dcm
-761.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0033.dcm
-766.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0034.dcm
-771.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0035.dcm
-776.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0036.dcm
-781.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0037.dcm
-786.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0038.dcm
-791.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0039.dcm
-796.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0040.dcm
-801.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0041.dcm
-806.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0042.dcm
-811.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0043.dcm
-816.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0044.dcm
-821.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0045.dcm
-826.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0046.dcm
-831.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0047.dcm
-836.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0048.dcm
-841.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0049.dcm
-846.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0050.dcm
-851.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0051.dcm
-856.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0052.dcm
-861.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0053.dcm
-866.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0054.dcm
-871.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0055.dcm
-876.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0056.dcm
-881.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0057.dcm
-886.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0058.dcm
-891.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0059.dcm
-896.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0060.dcm
-901.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0061.dcm
-906.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0062.dcm
-911.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0063.dcm
-916.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0064.dcm
-921.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0065.dcm
-926.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0066.dcm
-931.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0067.dcm
-936.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0068.dcm
-941.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0069.dcm
-946.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0070.dcm
-951.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0071.dcm
-956.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0072.dcm
-961.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0073.dcm
-966.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0074.dcm
-971.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0075.dcm
-976.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0076.dcm
-981.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0077.dcm
-986.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0078.dcm
-991.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0079.dcm
-996.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0080.dcm
-1001.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0081.dcm
-1006.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0082.dcm
-1011.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0083.dcm
-1016.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0084.dcm
-1021.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0085.dcm
-1026.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0086.dcm
-1031.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0087.dcm
-1036.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0088.dcm
-1041.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0089.dcm
-1046.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0090.dcm
-1051.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0091.dcm
-1056.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0092.dcm
-1061.6 C:\Users\miros/data/medical/orig/jatra_5mm\IM-0001-0093.dcm

















In [ ]:

Tables with pandas for analysis (we don't want to use pandas in io3d)





In [40]:



    


import pandas as pd
df = pd.DataFrame()

for filename in pths:
#     print(filename)
    dcmobj = pydicom.read_file(filename)
    df = df.append({
        "filename": filename, 
        "SliceLocation": dcmobj.SliceLocation,
        "ContentTime": dcmobj.ContentTime
    }, ignore_index=True)
#     print(filename)
df



    


















    
Out[40]:











  
    

      
      ContentTime
      SliceLocation
      filename
    

  
  
    

      0
      103644.875000
      -601.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      1
      103645.015000
      -606.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      2
      103645.187000
      -611.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      3
      103645.312000
      -616.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      4
      103645.468000
      -621.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      5
      103645.625000
      -626.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      6
      103645.781000
      -631.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      7
      103645.921000
      -636.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      8
      103646.109000
      -641.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      9
      103646.250000
      -646.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      10
      103646.546000
      -651.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      11
      103646.671000
      -656.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      12
      103646.828000
      -661.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      13
      103646.984000
      -666.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      14
      103647.140000
      -671.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      15
      103647.281000
      -676.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      16
      103647.468000
      -681.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      17
      103647.625000
      -686.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      18
      103647.781000
      -691.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      19
      103647.937000
      -696.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      20
      103648.093000
      -701.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      21
      103648.265000
      -706.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      22
      103648.421000
      -711.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      23
      103648.562000
      -716.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      24
      103648.718000
      -721.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      25
      103648.875000
      -726.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      26
      103649.015000
      -731.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      27
      103649.171000
      -736.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      28
      103649.343000
      -741.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      29
      103649.515000
      -746.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      ...
      ...
      ...
      ...
    

    

      63
      103655.000000
      -916.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      64
      103655.171000
      -921.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      65
      103655.328000
      -926.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      66
      103655.515000
      -931.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      67
      103655.671000
      -936.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      68
      103655.843000
      -941.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      69
      103656.031000
      -946.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      70
      103656.218000
      -951.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      71
      103656.375000
      -956.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      72
      103656.578000
      -961.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      73
      103656.734000
      -966.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      74
      103656.906000
      -971.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      75
      103657.062000
      -976.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      76
      103657.234000
      -981.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      77
      103657.421000
      -986.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      78
      103657.578000
      -991.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      79
      103657.750000
      -996.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      80
      103657.937000
      -1001.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      81
      103658.093000
      -1006.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      82
      103658.250000
      -1011.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      83
      103658.406000
      -1016.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      84
      103658.578000
      -1021.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      85
      103658.750000
      -1026.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      86
      103658.937000
      -1031.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      87
      103659.093000
      -1036.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      88
      103659.265000
      -1041.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      89
      103659.437000
      -1046.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      90
      103659.609000
      -1051.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      91
      103659.765000
      -1056.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

    

      92
      103659.937000
      -1061.6
      C:\Users\miros/data/medical/orig/jatra_5mm\IM-...
    

  



93 rows × 3 columns



















In [ ]:

Content source: mjirik/io3d

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