Error in 04_skeletonize.py: Function "parse_struc" was compiled in object mode without forceobj=True.

[Jan-No]

Hi,

first of all, thank you for this great project.

I tried to use the 04_skeletonize.py with images that I have created. This is one example image:

The make_skeleton() method runs perfectly and produces an excellent ske image as result.

However, the graph can't be generated, the output is:

len G.nodes(): 1
len G.edges(): 0

What am I doing wrong?

Thanks in advance for help.

Best,

Jan

PS: My configuration (main method). Values are taken from the sn5_baseline.json:

    log_file = '../results/skeleton.log'
    console, logger1 = make_logger.make_logger(log_file, logger_name='log')

    im_dir = "../data/"
    outfile_csv = "../results/out.csv"
    out_ske_dir = "../results/ske/"
    out_gdir = "../results/gdir/"

    debug = False
    add_small = True
    fix_borders = True
    img_shape = ()  # (1300, 1300)
    skel_replicate = 5
    skel_clip = 2
    img_mult = 255
    hole_size = 300
    cv2_kernel_close = 7
    cv2_kernel_open = 7
    # max_out_size=(16000, 8000)  # works fine
    # max_out_size=(8003, 16009)   # works fine
    max_out_size = (2000000, 2000000)
    spacenet_naming_convention = False

    # from config
    min_subgraph_length_pix = 20
    skeleton_band = 0
    num_classes= 1
    im_prefix = ''
    thresh = 0.3

    t0 = time.time()
    df = build_wkt_dir(im_dir, outfile_csv, out_ske_dir, out_gdir, thresh, #threshes={'2': .3, '3': .3, '4': .3, '5': .2},
                debug=debug, add_small=add_small, fix_borders=fix_borders,
                img_shape=img_shape,
                skel_replicate=skel_replicate, skel_clip=skel_clip,
                img_mult=img_mult, hole_size=hole_size,
                min_subgraph_length_pix=min_subgraph_length_pix,
                cv2_kernel_close=cv2_kernel_close, cv2_kernel_open=cv2_kernel_open,
                max_out_size=max_out_size,
                skeleton_band=skeleton_band,
                num_classes=num_classes,
                im_prefix=im_prefix,
                spacenet_naming_convention=spacenet_naming_convention)

    print ("len df:", len(df))
    print ("outfile:", outfile_csv)
    t1 = time.time()
    logger1.info("Total time to run build_wkt_dir: {} seconds".format(t1-t0))

PPS: The complete output:

 1 / 1 : prediction8.png
  img_loc: ../data/prediction8.png
  im_root: prediction8
  out_ske_file: ../results/ske/prediction8.png
Executing make_skeleton...
log     : INFO     1 / 1 : prediction8.png
make_skeleton(), input img_shape: ()
make_skeleton(), img.shape: (256, 256)
make_skeleton(), img.size: 65536
make_skeleton(), img dtype: uint8
run preprocess()...
Run preprocess() with skimage
Time to run preprocess(): 0.002991199493408203 seconds
skeletonize...
Time to run skimage.skeletonize(): 0.0019943714141845703 seconds
fix_borders...
Time fix borders: 0.0 seconds
ske.shape: (256, 256)
Time to run make_skeleton: 21.24360680580139 seconds
Execute sknw...
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:20: NumbaWarning: 
Compilation is falling back to object mode WITH looplifting enabled because Function "mark" failed type inference due to: Untyped global name 'neighbors': cannot determine Numba type of <class 'function'>

File "utils\sknw.py", line 22:
def mark(img):  # mark the array use (0, 1, 2)
    nbs = neighbors(img.shape)
    ^

  @jit  # my mark
numba.transforms: INFO     finding looplift candidates
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:20: NumbaWarning: 
Compilation is falling back to object mode WITHOUT looplifting enabled because Function "mark" failed type inference due to: Untyped global name 'neighbors': cannot determine Numba type of <class 'function'>

File "utils\sknw.py", line 22:
def mark(img):  # mark the array use (0, 1, 2)
    nbs = neighbors(img.shape)
    ^

  @jit  # my mark
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:178: NumbaWarning: Function "mark" was compiled in object mode without forceobj=True, but has lifted loops.

File "utils\sknw.py", line 22:
def mark(img):  # mark the array use (0, 1, 2)
    nbs = neighbors(img.shape)
    ^

  state.func_ir.loc))
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:188: NumbaDeprecationWarning: 
Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

File "utils\sknw.py", line 22:
def mark(img):  # mark the array use (0, 1, 2)
    nbs = neighbors(img.shape)
    ^

  state.func_ir.loc))
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:92: NumbaWarning: 
Compilation is falling back to object mode WITH looplifting enabled because Function "parse_struc" failed type inference due to: Untyped global name 'neighbors': cannot determine Numba type of <class 'function'>

File "utils\sknw.py", line 94:
def parse_struc(img):
    nbs = neighbors(img.shape)
    ^

  @jit  # parse the image then get the nodes and edges
numba.transforms: INFO     finding looplift candidates
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:92: NumbaWarning: 
Compilation is falling back to object mode WITHOUT looplifting enabled because Function "parse_struc" failed type inference due to: Untyped global name 'neighbors': cannot determine Numba type of <class 'function'>

File "utils\sknw.py", line 94:
def parse_struc(img):
    nbs = neighbors(img.shape)
    ^

  @jit  # parse the image then get the nodes and edges
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:178: NumbaWarning: Function "parse_struc" was compiled in object mode without forceobj=True, but has lifted loops.

File "utils\sknw.py", line 94:
def parse_struc(img):
    nbs = neighbors(img.shape)
    ^

  state.func_ir.loc))
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:188: NumbaDeprecationWarning: 
Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

File "utils\sknw.py", line 94:
def parse_struc(img):
    nbs = neighbors(img.shape)
    ^

  state.func_ir.loc))
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:92: NumbaWarning: 
Compilation is falling back to object mode WITHOUT looplifting enabled because Function "parse_struc" failed type inference due to: non-precise type pyobject
[1] During: typing of argument at C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py (101)

File "utils\sknw.py", line 101:
def parse_struc(img):
    <source elided>
    nodes = []
    for p in pts:
    ^

  @jit  # parse the image then get the nodes and edges
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:178: NumbaWarning: Function "parse_struc" was compiled in object mode without forceobj=True.

File "utils\sknw.py", line 101:
def parse_struc(img):
    <source elided>
    nodes = []
    for p in pts:
    ^

  state.func_ir.loc))
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:188: NumbaDeprecationWarning: 
Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

File "utils\sknw.py", line 101:
def parse_struc(img):
    <source elided>
    nodes = []
    for p in pts:
    ^

  state.func_ir.loc))
C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py:92: NumbaWarning: 
Compilation is falling back to object mode WITHOUT looplifting enabled because Function "parse_struc" failed type inference due to: non-precise type pyobject
[1] During: typing of argument at C:\Users\Jan.noessner\Documents\01_road_detection\resources\centerline\cresi\cresi\utils\sknw.py (108)

File "utils\sknw.py", line 108:
def parse_struc(img):
    <source elided>
    edges = []
    for p in pts:
    ^

  @jit  # parse the image then get the nodes and edges
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:178: NumbaWarning: Function "parse_struc" was compiled in object mode without forceobj=True.

File "utils\sknw.py", line 108:
def parse_struc(img):
    <source elided>
    edges = []
    for p in pts:
    ^

  state.func_ir.loc))
C:\Apps\Anaconda3\envs\ml\lib\site-packages\numba\object_mode_passes.py:188: NumbaDeprecationWarning: 
Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.

For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit

File "utils\sknw.py", line 108:
def parse_struc(img):
    <source elided>
    edges = []
    for p in pts:
    ^

  state.func_ir.loc))
log     : INFO     Time to build graph: 1018.8935737609863 seconds
log     : INFO     Total time to run build_wkt_dir: 1018.8965332508087 seconds
len G.nodes(): 1
len G.edges(): 0
len df: 1
outfile: ../results/out.csv

Process finished with exit code 0