Setup.py Failed toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found #172

andreeaboiciuc · 2024-11-25T11:19:54Z

Issue: Compiling NanoTracker Setup

Description

Hello there! I'm trying to use the train for NanoTracker. I have installed all the necessary packages from the requirements with default versions for Python 3.12. I am running Ubuntu 24.04. Below is the list of installed package versions:

Package	Version
torch	2.5.1+cu121
torchvision	0.20.1+cu121
torchaudio	2.5.1+cu121
matplotlib	3.9.2
pandas	2.2.3
opencv-python	4.10.0.84
tensorboardX	2.6.2.2
Cython	3.0.11
yacs	0.1.8
scikit-image	0.24.0
pillow	11.0.0
scipy	1.14.1
shapely	2.0.6
tqdm	4.67.1
easydict	1.13
jpeg4py	0.1.4
mpi4py	4.0.1
ray	2.39.0
hyperopt	0.2.7

Steps to Reproduce

Clone the NanoTracker repository.
Install dependencies using the requirements file.
Run the following command to build:
```
python setup.py build_ext --inplace
```

After I want to make the build :

but i have this issue:

python setup.py build_ext --inplace
Compiling toolkit/utils/region.pyx because it changed.
[1/1] Cythonizing toolkit/utils/region.pyx

Error compiling Cython file:

...

from libc.stdlib cimport malloc, free
from libc.stdio cimport sprintf
from libc.string cimport strlen

cimport c_region
^

toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found

Error compiling Cython file:

...
RECTANGEL
POLYGON
MASK

cdef class RegionBounds:
cdef c_region.region_bounds* _c_region_bounds
^

toolkit/utils/region.pyx:21:9: 'region_bounds' is not a type identifier

Error compiling Cython file:

...
self._c_region_bounds.bottom = bottom
self._c_region_bounds.left = left
self._c_region_bounds.right = right

cdef class Rectangle:
cdef c_region.region_rectangle* _c_region_rectangle
^

toolkit/utils/region.pyx:58:9: 'region_rectangle' is not a type identifier

Error compiling Cython file:

...
self._c_region_rectangle.y,
self._c_region_rectangle.width,
self._c_region_rectangle.height)

cdef class Polygon:
cdef c_region.region_polygon* _c_region_polygon
^

toolkit/utils/region.pyx:99:9: 'region_polygon' is not a type identifier

Error compiling Cython file:

...
else:
pno_bounds = RegionBounds(-float("inf"), float("inf"),
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_._c_region_polygon
^

toolkit/utils/region.pyx:182:9: 'region_polygon' is not a type identifier

Error compiling Cython file:

...
pno_bounds = RegionBounds(-float("inf"), float("inf"),
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon
cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon
^

toolkit/utils/region.pyx:183:9: 'region_polygon' is not a type identifier

Error compiling Cython file:

...
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon
cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon
cdef c_region.region_bounds no_bounds = pno_bounds._c_region_bounds[0] # deference
^

toolkit/utils/region.pyx:184:9: 'region_bounds' is not a type identifier

Error compiling Cython file:

...

cdef class RegionBounds:
cdef c_region.region_bounds* _c_region_bounds

def cinit(self):
self._c_region_bounds = <c_region.region_bounds*>malloc(
^

toolkit/utils/region.pyx:24:33: 'region_bounds' is not a type identifier

Error compiling Cython file:

...
cdef class RegionBounds:
cdef c_region.region_bounds* _c_region_bounds

def cinit(self):
self._c_region_bounds = <c_region.region_bounds*>malloc(
sizeof(c_region.region_bounds))
^

toolkit/utils/region.pyx:25:32: cimported module has no attribute 'region_bounds'

Error compiling Cython file:

...

cdef class Rectangle:
cdef c_region.region_rectangle* _c_region_rectangle

def cinit(self):
self._c_region_rectangle = <c_region.region_rectangle*>malloc(
^

toolkit/utils/region.pyx:61:36: 'region_rectangle' is not a type identifier

Error compiling Cython file:

...
cdef class Rectangle:
cdef c_region.region_rectangle* _c_region_rectangle

def cinit(self):
self._c_region_rectangle = <c_region.region_rectangle*>malloc(
sizeof(c_region.region_rectangle))
^

toolkit/utils/region.pyx:62:32: cimported module has no attribute 'region_rectangle'

Error compiling Cython file:

...
args:
points: tuple of point
points = ((1, 1), (10, 10))
"""
num = len(points) // 2
self._c_region_polygon = <c_region.region_polygon*>malloc(
^

toolkit/utils/region.pyx:108:34: 'region_polygon' is not a type identifier

Error compiling Cython file:

...
points: tuple of point
points = ((1, 1), (10, 10))
"""
num = len(points) // 2
self._c_region_polygon = <c_region.region_polygon*>malloc(
sizeof(c_region.region_polygon))
^

toolkit/utils/region.pyx:109:32: cimported module has no attribute 'region_polygon'

Error compiling Cython file:

...
sizeof(c_region.region_polygon))
if not self._c_region_polygon:
self._c_region_polygon = NULL
raise MemoryError()
self._c_region_polygon.count = num
self._c_region_polygon.x = <float>malloc(sizeof(float) num)
^

toolkit/utils/region.pyx:114:35: Cannot convert 'float *' to Python object

Error compiling Cython file:

...
raise MemoryError()
self._c_region_polygon.count = num
self._c_region_polygon.x = <float>malloc(sizeof(float) num)
if not self._c_region_polygon.x:
raise MemoryError()
self._c_region_polygon.y = <float>malloc(sizeof(float) num)
^

toolkit/utils/region.pyx:117:35: Cannot convert 'float *' to Python object

Error compiling Cython file:

...
self._c_region_polygon.x[i] = points[i2]
self._c_region_polygon.y[i] = points[i2+1]

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
^

toolkit/utils/region.pyx:127:40: Invalid types for 'is_not' (Python object, void *)

Error compiling Cython file:

...
self._c_region_polygon.y[i] = points[i*2+1]

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
^

toolkit/utils/region.pyx:128:43: Cannot convert Python object to 'void *'

Error compiling Cython file:

...

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
^

toolkit/utils/region.pyx:129:43: Cannot convert 'void *' to Python object

Error compiling Cython file:

...
def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
^

toolkit/utils/region.pyx:130:40: Invalid types for 'is_not' (Python object, void *)

Error compiling Cython file:

...
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
free(self._c_region_polygon.y)
^

toolkit/utils/region.pyx:131:43: Cannot convert Python object to 'void *'

Error compiling Cython file:

...
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
free(self._c_region_polygon.y)
self._c_region_polygon.y = NULL
^

toolkit/utils/region.pyx:132:43: Cannot convert 'void *' to Python object

Error compiling Cython file:

...
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon
cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon
cdef c_region.region_bounds no_bounds = pno_bounds._c_region_bounds[0] # deference
return c_region.compute_polygon_overlap(c_polygon1,
^

toolkit/utils/region.pyx:185:19: cimported module has no attribute 'compute_polygon_overlap'

Traceback (most recent call last):
File "/home/andreea/Documents/SiamTrackers/NanoTrack/setup.py", line 22, in
ext_modules=cythonize(
^^^^^^^^^^
File "/home/andreea/tracker/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/home/andreea/tracker/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: toolkit/utils/region.pyx

mention that the files are present in the belonging folder/folders. toolkit/utils/ and toolkit/utils/src .So i don't get why the issue persists. Can you please indicate what the issue could be to be able to make the train? Thanks a lot in advance .

733ly · 2024-12-16T14:15:14Z

I have the same problem！！

XY-ZXY · 2025-01-02T04:46:11Z

可以试一试将Cython的版本退回0.29.21

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Setup.py Failed toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found #172

Setup.py Failed toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found #172

andreeaboiciuc commented Nov 25, 2024 •

edited

Loading

733ly commented Dec 16, 2024

XY-ZXY commented Jan 2, 2025

Setup.py Failed toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found #172

Setup.py Failed toolkit/utils/region.pyx:11:8: 'c_region.pxd' not found #172

Comments

andreeaboiciuc commented Nov 25, 2024 • edited Loading

Issue: Compiling NanoTracker Setup

Description

Steps to Reproduce

Error compiling Cython file:

cimport c_region ^

Error compiling Cython file:

cdef class RegionBounds: cdef c_region.region_bounds* _c_region_bounds ^

Error compiling Cython file:

cdef class Rectangle: cdef c_region.region_rectangle* _c_region_rectangle ^

Error compiling Cython file:

cdef class Polygon: cdef c_region.region_polygon* _c_region_polygon ^

Error compiling Cython file:

... else: pno_bounds = RegionBounds(-float("inf"), float("inf"), -float("inf"), float("inf")) cdef float only1 = 0 cdef float only2 = 0 cdef c_region.region_polygon* c_polygon1 = polygon1_._c_region_polygon ^

Error compiling Cython file:

... pno_bounds = RegionBounds(-float("inf"), float("inf"), -float("inf"), float("inf")) cdef float only1 = 0 cdef float only2 = 0 cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon ^

Error compiling Cython file:

... -float("inf"), float("inf")) cdef float only1 = 0 cdef float only2 = 0 cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon cdef c_region.region_bounds no_bounds = pno_bounds._c_region_bounds[0] # deference ^

Error compiling Cython file:

def cinit(self): self._c_region_bounds = <c_region.region_bounds*>malloc( ^

Error compiling Cython file:

def cinit(self): self._c_region_bounds = <c_region.region_bounds*>malloc( sizeof(c_region.region_bounds)) ^

Error compiling Cython file:

def cinit(self): self._c_region_rectangle = <c_region.region_rectangle*>malloc( ^

Error compiling Cython file:

def cinit(self): self._c_region_rectangle = <c_region.region_rectangle*>malloc( sizeof(c_region.region_rectangle)) ^

Error compiling Cython file:

... args: points: tuple of point points = ((1, 1), (10, 10)) """ num = len(points) // 2 self._c_region_polygon = <c_region.region_polygon*>malloc( ^

Error compiling Cython file:

... points: tuple of point points = ((1, 1), (10, 10)) """ num = len(points) // 2 self._c_region_polygon = <c_region.region_polygon*>malloc( sizeof(c_region.region_polygon)) ^

Error compiling Cython file:

... sizeof(c_region.region_polygon)) if not self._c_region_polygon: self._c_region_polygon = NULL raise MemoryError() self._c_region_polygon.count = num self._c_region_polygon.x = <float*>malloc(sizeof(float) * num) ^

Error compiling Cython file:

... raise MemoryError() self._c_region_polygon.count = num self._c_region_polygon.x = <float*>malloc(sizeof(float) * num) if not self._c_region_polygon.x: raise MemoryError() self._c_region_polygon.y = <float*>malloc(sizeof(float) * num) ^

Error compiling Cython file:

def dealloc(self): if self._c_region_polygon is not NULL: if self._c_region_polygon.x is not NULL: ^

Error compiling Cython file:

def dealloc(self): if self._c_region_polygon is not NULL: if self._c_region_polygon.x is not NULL: free(self._c_region_polygon.x) ^

Error compiling Cython file:

def dealloc(self): if self._c_region_polygon is not NULL: if self._c_region_polygon.x is not NULL: free(self._c_region_polygon.x) self._c_region_polygon.x = NULL ^

Error compiling Cython file:

... def dealloc(self): if self._c_region_polygon is not NULL: if self._c_region_polygon.x is not NULL: free(self._c_region_polygon.x) self._c_region_polygon.x = NULL if self._c_region_polygon.y is not NULL: ^

Error compiling Cython file:

... if self._c_region_polygon is not NULL: if self._c_region_polygon.x is not NULL: free(self._c_region_polygon.x) self._c_region_polygon.x = NULL if self._c_region_polygon.y is not NULL: free(self._c_region_polygon.y) ^

Error compiling Cython file:

... if self._c_region_polygon.x is not NULL: free(self._c_region_polygon.x) self._c_region_polygon.x = NULL if self._c_region_polygon.y is not NULL: free(self._c_region_polygon.y) self._c_region_polygon.y = NULL ^

Error compiling Cython file:

733ly commented Dec 16, 2024

XY-ZXY commented Jan 2, 2025

andreeaboiciuc commented Nov 25, 2024 •

edited

Loading

cimport c_region
^

cdef class RegionBounds:
cdef c_region.region_bounds* _c_region_bounds
^

cdef class Rectangle:
cdef c_region.region_rectangle* _c_region_rectangle
^

cdef class Polygon:
cdef c_region.region_polygon* _c_region_polygon
^

...
else:
pno_bounds = RegionBounds(-float("inf"), float("inf"),
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_._c_region_polygon
^

...
pno_bounds = RegionBounds(-float("inf"), float("inf"),
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon
cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon
^

...
-float("inf"), float("inf"))
cdef float only1 = 0
cdef float only2 = 0
cdef c_region.region_polygon* c_polygon1 = polygon1_.c_region_polygon
cdef c_region.region_polygon* c_polygon2 = polygon2._c_region_polygon
cdef c_region.region_bounds no_bounds = pno_bounds._c_region_bounds[0] # deference
^

def cinit(self):
self._c_region_bounds = <c_region.region_bounds*>malloc(
^

def cinit(self):
self._c_region_bounds = <c_region.region_bounds*>malloc(
sizeof(c_region.region_bounds))
^

def cinit(self):
self._c_region_rectangle = <c_region.region_rectangle*>malloc(
^

def cinit(self):
self._c_region_rectangle = <c_region.region_rectangle*>malloc(
sizeof(c_region.region_rectangle))
^

...
args:
points: tuple of point
points = ((1, 1), (10, 10))
"""
num = len(points) // 2
self._c_region_polygon = <c_region.region_polygon*>malloc(
^

...
points: tuple of point
points = ((1, 1), (10, 10))
"""
num = len(points) // 2
self._c_region_polygon = <c_region.region_polygon*>malloc(
sizeof(c_region.region_polygon))
^

...
sizeof(c_region.region_polygon))
if not self._c_region_polygon:
self._c_region_polygon = NULL
raise MemoryError()
self._c_region_polygon.count = num
self._c_region_polygon.x = <float>malloc(sizeof(float) num)
^

...
raise MemoryError()
self._c_region_polygon.count = num
self._c_region_polygon.x = <float>malloc(sizeof(float) num)
if not self._c_region_polygon.x:
raise MemoryError()
self._c_region_polygon.y = <float>malloc(sizeof(float) num)
^

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
^

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
^

def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
^

...
def dealloc(self):
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
^

...
if self._c_region_polygon is not NULL:
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
free(self._c_region_polygon.y)
^

...
if self._c_region_polygon.x is not NULL:
free(self._c_region_polygon.x)
self._c_region_polygon.x = NULL
if self._c_region_polygon.y is not NULL:
free(self._c_region_polygon.y)
self._c_region_polygon.y = NULL
^