Exception in create_distance_map in Windows

[phcerdan]

Reported in https://discourse.vtk.org/t/vmtk-center-lines-extraction-how-to-accelerate-it-and-how-to-extract-center-lines-from-small-vessel/4103/13

sgextImg = sgext.itk.IUC3P()
sgextImg.from_pyarray(mask*255)
dmap_image = sgext.scripts.create_distance_map(input=sgextImg, verbose=True)
thin_image = sgext.scripts.thin(input=sgextImg,
                   table_folder= sgext.tables_folder,
                   skel_type="end",
                   select_type="dmax",
                   input_distance_map_image=dmap_image,
                   persistence=2,
                   visualize=False,
                   verbose=True
                   )

dmap_image = sgext.scripts.create_distance_map(input=sgextImg, verbose=True)

unhandled win32 exception occurred in python.exe

My environment is:

win10
Python 3.7.5 (default, Oct 31 2019, 15:18:51) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
sgext: I don't know the version. I think it is the latest version.

[NeuZhangQiang]

How can I get more verbose error about that exception?

dmap_image = sgext.scripts.create_distance_map(input=sgextImg, verbose=True)

This code cause a vs bug. And the picture is:

I am sorry that the character is Chinese. But it means:

unhandled win32 exception occurred in python.exe

[phcerdan]

I am not sure to be honest, let me try to reproduce it. Thanks for your time on this.

[phcerdan]

@NeuZhangQiang you could try meanwhile with:

sgextImg = sgext.itk.IUC3P()
sgextImg.from_pyarray(mask*255)
dmap_image = sgext.itk.IF3P()
thin_image = sgext.scripts.thin(input=sgextImg,
                   table_folder= sgext.tables_folder,
                   skel_type="end",
                   select_type="first",
                   input_distance_map_image=dmap_image,
                   persistence=2,
                   visualize=False,
                   verbose=True
                   )

I have changed select_type to "first" and dmap_image is initialized to an empty image.
This will be solved in the next release.

I will explore meanwhile the exception in create_distance_map.

[NeuZhangQiang]

I have tested the following code:

mask = np.zeros(shape=[500, 500, 400], dtype=np.uint8)
mask[250:350, 250:350, 100:300] = 255
sgextImg = sgext.itk.IUC3P()
sgextImg.from_pyarray(mask)
dmap_image = sgext.itk.IF3P()
thin_image = sgext.scripts.thin(input=sgextImg,
                   table_folder= sgext.tables_folder,
                   skel_type="end",
                   select_type="first",
                   input_distance_map_image=dmap_image,
                   persistence=2,
                   visualize=False,
                   verbose=True
                   )

And the bug is:

TypeError: thin(): incompatible function arguments. The following argument types are supported:
    1. (input: itk::SmartPointer<itk::Image<unsigned char,3> >, skel_type: str, select_type: str, tables_folder: str, persistence: int = 0, input_distance_map_image: itk::SmartPointer<itk::Image<float,3> > = None, profile: bool = False, verbose: bool = False, visualize: bool = False) -> itk::SmartPointer<itk::Image<unsigned char,3> >

Invoked with: kwargs: input=Dimension: 3
LargestPossibleRegion: 
  Index: [0, 0, 0]
  Size (i,j,k) (c_array): [400, 500, 500]
Origin: [0, 0, 0]
Spacing: [1, 1, 1]
Direction: 
1 0 0
0 1 0
0 0 1
Buffer: 
ImportImageContainer (00000292CCE157E0)
  RTTI typeinfo:   class itk::ImportImageContainer<unsigned __int64,unsigned char>
  Reference Count: 1
  Modified Time: 56
  Debug: Off
  Object Name: 
  Observers: 
    none
  Pointer: 00000292CE1AB040
  Container manages memory: false
  Size: 100000000
  Capacity: 100000000
, table_folder='D:\\ProgramData\\Anaconda3\\envs\\general\\lib\\site-packages\\sgext\\tables', skel_type='end', select_type='first', input_distance_map_image=Dimension: 3
LargestPossibleRegion: 
  Index: [0, 0, 0]
  Size (i,j,k) (c_array): [0, 0, 0]
Origin: [0, 0, 0]
Spacing: [1, 1, 1]
Direction: 
1 0 0
0 1 0
0 0 1
Buffer: 
ImportImageContainer (00000292CCE138E0)
  RTTI typeinfo:   class itk::ImportImageContainer<unsigned __int64,float>
  Reference Count: 1
  Modified Time: 66
  Debug: Off
  Object Name: 
  Observers: 
    none
  Pointer: 0000000000000000
  Container manages memory: true
  Size: 0
  Capacity: 0
, persistence=2, visualize=False, verbose=True

[phcerdan]

Ok, I will release the next version of sgext today to solve the latest one.

Umm, could you try the version with the distance map, but in a much smaller image, just in case the exception is related to memory:

mask = np.zeros(shape=[50, 50, 40], dtype=np.uint8)
mask[25:35, 25:35, 10:30] = 255
sgextImg.from_pyarray(mask)
dmap_image = sgext.scripts.create_distance_map(input=sgextImg, verbose=True)
thin_image = sgext.scripts.thin(input=sgextImg,
                   table_folder= sgext.tables_folder,
                   skel_type="end",
                   select_type="dmax",
                   input_distance_map_image=dmap_image,
                   persistence=2,
                   visualize=False,
                   verbose=True
                   )

[phcerdan]

I cannot reproduce it, have you checked if it was a memory problem? Let me know

[NeuZhangQiang]

I have run the following code:

mask = np.zeros(shape=[50, 50, 40], dtype=np.uint8)
mask[25:35, 25:35, 10:30] = 255

sgextImg = sgext.itk.IUC3P()
sgextImg.from_pyarray(mask)
# dmap_image = sgext.itk.IF3P()
dmap_image = sgext.scripts.create_distance_map(input=sgextImg, verbose=True)
thin_image = sgext.scripts.thin(input=sgextImg,
                   table_folder= sgext.tables_folder,
                   skel_type="end",
                   select_type="dmax",
                   input_distance_map_image=dmap_image,
                   persistence=2,
                   visualize=False,
                   verbose=True
                   )

But the bug is still reported:

New Block [Create Distance Map]
EndBlock [Create Distance Map] (39 ms)
Traceback (most recent call last):
  File "E:/Keypoint/data/bronchi/sgextScript.py", line 24, in <module>
    verbose=True
TypeError: thin(): incompatible function arguments. The following argument types are supported:
    1. (input: itk::SmartPointer<itk::Image<unsigned char,3> >, skel_type: str, select_type: str, tables_folder: str, persistence: int = 0, input_distance_map_image: itk::SmartPointer<itk::Image<float,3> > = None, profile: bool = False, verbose: bool = False, visualize: bool = False) -> itk::SmartPointer<itk::Image<unsigned char,3> >

Invoked with: kwargs: input=Dimension: 3
LargestPossibleRegion: 
  Index: [0, 0, 0]
  Size (i,j,k) (c_array): [40, 50, 50]
Origin: [0, 0, 0]
Spacing: [1, 1, 1]
Direction: 
1 0 0
0 1 0
0 0 1
Buffer: 
ImportImageContainer (000002BAB2E45FE0)
  RTTI typeinfo:   class itk::ImportImageContainer<unsigned __int64,unsigned char>
  Reference Count: 1
  Modified Time: 56
  Debug: Off
  Object Name: 
  Observers: 
    none
  Pointer: 000002BAB36E5F00
  Container manages memory: false
  Size: 100000
  Capacity: 100000
, table_folder='D:\\ProgramData\\Anaconda3\\envs\\general\\lib\\site-packages\\sgext\\tables', skel_type='end', select_type='dmax', input_distance_map_image=Dimension: 3
LargestPossibleRegion: 
  Index: [0, 0, 0]
  Size (i,j,k) (c_array): [40, 50, 50]
Origin: [0, 0, 0]
Spacing: [1, 1, 1]
Direction: 
1 0 0
0 1 0
0 0 1
Buffer: 
ImportImageContainer (000002BAB2E47F60)
  RTTI typeinfo:   class itk::ImportImageContainer<unsigned __int64,float>
  Reference Count: 1
  Modified Time: 69
  Debug: Off
  Object Name: 
  Observers: 
    none
  Pointer: 000002BAB3757D30
  Container manages memory: true
  Size: 100000
  Capacity: 100000
, persistence=2, visualize=False, verbose=True
Time elapsed: 0

The environment is:

win10, 32 GB memory
Python 3.7.5 (default, Oct 31 2019, 15:18:51) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
sgext-0.9.12

And I think it is not a memory problem.

[phcerdan]

Please update sgext: pip install --upgrade sgext to solve the thin(): incompatible function arguments error. Fixed in 29cdaa2.

I am closing this issue, you were able to create_distance_map in windows with no exception.

[vijosam]

@phcerdan Thanks for sharing your wonderful package. I notice that the lastest version in pypi is 0.9.13 and the incompatible function arguments error in thin() also exists. Could you fix this?

[phcerdan]

@LydiaLS That error could be triggered for many parameters, please open a new issue, post the minimal code that you are using, and the platform. Thanks!