Commit e56bda2f authored by Oleg Dzhimiev's avatar Oleg Dzhimiev
Browse files

refactored, tested for 3D,4D and 5D

parent 8b48ba4a

imagej_tiffwriter.py

+23 −11
Original line number Diff line number Diff line
@@ -81,10 +81,9 @@ def save(path,images): 


  # 0 or 1 images.shapes are not handled

  #

  # save single channel image in the form of numpy array

  #   -

  # (h,w)

  if len(images.shape)==2:

    # (h,w) -> (h,w,c=1)



    image = Image.fromarray(images)

    image.save(path)
@@ -102,15 +101,14 @@ def save(path,images): 


    t  = images.shape[-5]



    c_axis = len(images.shape)-1

    c_axis = -1



    if c>1:

      channels = np.squeeze(np.split(images,c,axis=c_axis))

    if c==1:

      split_channels = images

    else:

      channels = np.squeeze(images,axis=c_axis)





      channels = np.array(np.split(images,c,axis=c_axis))

      split_channels = np.concatenate(channels,axis=-3)



    images_flat = np.reshape(split_channels,(-1,h,w))



    imlist = []
@@ -147,4 +145,18 @@ if __name__ == "__main__": 
  print(str(time.time())+": Test images generated")

  print("Images shape: "+str(images.shape))



  v = save("result_2.tiff",images)
 
  print("5D run")

  v = save("result_5D.tiff",images)

  print("4D run")

  v = save("result_4D.tiff",images[0])

  print("3D run")

  v = save("result_3D.tiff",images[0,0])

  print("3D run, 1 channel")

  tmp_images = images[0,0,:,:,0]

  v = save("result_3D1C.tiff",tmp_images[:,:,np.newaxis])