How can i combine or concatenated generated multiple series of DICOM image into single frame?

[Yuvi-416]

Hi there,
I am looking for some suggestion regarding my problem.
I was able to convert a number of png image into DICOM and now I want to concatenate them into a single frame. How can I achieve that?
Any suggestion

[scaramallion]

Just do the normal numpy array concatenation.

arr1 = np.asarray([[1, 2], [3, 4]])
arr2 = np.asarray([[5, 6], [7, 8]])

arr = np.concatenate((arr1, arr2), axis=1)
ds.Rows, ds.Columns = arr.shape
ds.PixelData = arr.tobytes()
# etc...

[Yuvi-416]

Hi there,
You mean to say I should concatenate before generating multiple series DCM files or after generating multiple series files.
I am following below code:

import numpy as np
import pydicom
import os
from natsort import natsorted

Multiple_series_DICOM_Image = "/home/Channel_-01-0/"
Single_frame_DICOM_Image = "/home/Single_frame_output/"
# Read a dicom multiple series files one by one
iii = []
names = os.listdir(Multiple_series_DICOM_Image)
# names = natsorted(names)
names = sorted(names, key=lambda i: int(os.path.splitext(os.path.basename(i))[0]))
for file_name in names:
    if file_name.endswith(".dcm"):
        filename, file_extension = os.path.splitext(file_name)
        dicom_meta = pydicom.dcmread(Multiple_series_DICOM_Image + "/" + file_name, force=True)
        image_dcm = dicom_meta.pixel_array
        # arr = np.concatenate(image_dcm)
        iii.append(image_dcm)

But I couldn't understand how can I add 120 images pixe_array

[scaramallion]

I have no idea what you're trying to do, so 🤷‍♂️

[Gowtham58]

A python function that could help.

This is when you have a single .dcm file with multiple slides in it. Just pass the path string to the function. and also replace png_path with a path to save the PNG.

from PIL import Image
from pydicom import dcmread

def dicom2png(self, path:str) -> np.array:
    dimage = dcmread(path)
    darray = dimage.pixel_array
    if len(darray.shape)==4:
      ddim = darray.shape[0]*darray.shape[1]*darray.shape[2]
      v_mrg = []
      h_mrg = darray[0]
      for i in range(1,darray.shape[0]):
        if h_mrg.shape[1]>=int(math.sqrt(ddim)):
          v_mrg.append(h_mrg[:,:-int(h_mrg.shape[0])])
          h_mrg = darray[i]
          continue
        h_mrg = np.concatenate((h_mrg, darray[i]), axis =1)

      img = v_mrg[0]
      for i in v_mrg[1:]:
        img = np.concatenate((img, i))

    else:
      img = darray
    PIL_image = Image.fromarray(img_png.astype('uint8'), 'RGB')
    PIL_image.save(png_path)

If you have a folder of single .dmc files, may be you can read each file separetely and append it to an array and make it the darray variable in the function.

Hope this helps.