Ytukyg

I am trying to do a project. Unfortuantely I can read the dicom files, but when I try to access pixel_array attribute and plot it, it is throwing error.

def readDcm(self):

        #path of the decomFolder

        print("Path to the DICOM directory is: ",self.dcmPath)

        PathDicom = self.dcmPath

        lstFilesDCM =   # creating an empty list

        for dirName, subdirList, fileList in os.walk(PathDicom):

            for filename in fileList:

                if ".dcm" in filename.lower():  # checking whether the file's DICOM

                    lstFilesDCM.append(os.path.join(dirName,filename))





        print(len(lstFilesDCM))



        for filename in lstFilesDCM:

            currentDcm = pydicom.read_file(lstFilesDCM[0])

            dcm_data = currentDcm.PixelData

            pixeldata= currentDcm.pixel_array

the error is:

File "C:Anaconda3libsite-packagespydicompixel_data_handlerspillow_handler.py", line 199, in get_pixeldata

    raise NotImplementedError(e.strerror)



NotImplementedError: None

Any suggestion would be nice. Thank you in advance.

Solved Solution:

def load_scan(path):

    slices = [dicom.read_file(path + '/' + s) for s in os.listdir(path)]

    slices.sort(key = lambda x: float(x.ImagePositionPatient[2]))

    pos1 = slices[int(len(slices)/2)].ImagePositionPatient[2]

    pos2 = slices[(int(len(slices)/2)) + 1].ImagePositionPatient[2]

    diff = pos2 - pos1

    if diff > 0:

        slices = np.flipud(slices)

    try:

        slice_thickness = np.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])

    except:

        slice_thickness = np.abs(slices[0].SliceLocation - slices[1].SliceLocation)



    for s in slices:

        s.SliceThickness = slice_thickness

    return slices 

Without any further context, it's difficult to assert anything. However, when I look at the way you collect the potential DICOM files, you are probably constructing not existing path (it looks like you skip one hierarchy level when joining path parts back; you may want to check that the constructed path actually points to an existing files using os.path.exists()).

You may want to change the iterating part:

    for dirName, subdirList, fileList in os.walk(PathDicom):

        for filename in fileList:

            if ".dcm" in filename.lower():  # checking whether the file's DICOM

                lstFilesDCM.append(os.path.join(dirName,filename)) # <-you cut one potential hierarchy level

with something like:

dicom_files = 

for d, dirs, files in os.walk('./data/'):

    for x in files:

        if x.endswith(".png"):

            dicom_path = os.path.join(d, x)

            if os.path.exists(dicom_path):

                dicom_files.append(dicom_path)

I sorted the dicom files according to the axis which was in increasing order by using ImagePositionPatient attribute. Which solved my problem. I was able to access pixel_array attribute and plot. The code is added to original question. I add it below too.

def load_scan(path):

    slices = [dicom.read_file(path + '/' + s) for s in os.listdir(path)]

    slices.sort(key = lambda x: float(x.ImagePositionPatient[2]))

    pos1 = slices[int(len(slices)/2)].ImagePositionPatient[2]

    pos2 = slices[(int(len(slices)/2)) + 1].ImagePositionPatient[2]

    diff = pos2 - pos1

    if diff > 0:

        slices = np.flipud(slices)

    try:

        slice_thickness = np.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])

    except:

        slice_thickness = np.abs(slices[0].SliceLocation - slices[1].SliceLocation)



    for s in slices:

        s.SliceThickness = slice_thickness

    return slices 

code source:https://www.programcreek.com/python/example/97517/dicom.read_file