jni / llc-tools

Decorators to make it easier to write SciPy LowLevelCallables

llc-tools

Decorators to make it easier to write SciPy LowLevelCallables

llc-tools's Issues

Add docstrings to all the functions

The functions in llc-tools are not even documented themselves. It would be good to change that. See the Guide to NumPy documentation:

https://numpy.org/doc/stable/docs/howto_document.html

Create documentation on ReadTheDocs

The two blog posts that motivated this library contain some useful references for documentation:

https://ilovesymposia.com/2017/03/12/scipys-new-lowlevelcallable-is-a-game-changer/

https://ilovesymposia.com/2017/03/15/prettier-lowlevelcallables-with-numba-jit-and-decorators/

Currently, llc-tools doesn't have any documentation. It would be good to put some on ReadTheDocs or GitHub Pages.

Other useful references:

https://docs.scipy.org/doc/scipy/reference/generated/scipy.LowLevelCallable.from_cython.html

https://docs.scipy.org/doc/scipy/reference/ccallback.html

Sample code on your blog not working

I followed your code on https://ilovesymposia.com/2017/03/15/prettier-lowlevelcallables-with-numba-jit-and-decorators/

import numba
from numba import cfunc, carray, jit
from numba.types import intc, CPointer, float64, intp, voidptr, uint8
from scipy import LowLevelCallable

def jit_filter_function(filter_function):
    """Decorator for use with scipy.ndimage.generic_filter."""
    jitted_function = numba.jit(filter_function, nopython=True)

    @cfunc(intc(CPointer(float64), intp, CPointer(float64), voidptr))
    def wrapped(values_ptr, len_values, result, data):
        values = carray(values_ptr, (len_values,), dtype=float64)
        result[0] = jitted_function(values)
        return 1
    return LowLevelCallable(wrapped.ctypes)

@jit_filter_function
def fmin(values):
    result = np.inf
    for v in values:
        if v < result:
            result = v

Encountered the following error

LoweringError: Caused By:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 238, in run
    stage()
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 644, in stage_nopython_backend
    self._backend(lowerfn, objectmode=False)
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 599, in _backend
    lowered = lowerfn()
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 586, in backend_nopython_mode
    self.flags)
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 882, in native_lowering_stage
    lower.lower()
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 135, in lower
    self.lower_normal_function(self.fndesc)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 176, in lower_normal_function
    entry_block_tail = self.lower_function_body()
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 201, in lower_function_body
    self.lower_block(block)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 216, in lower_block
    self.lower_inst(inst)
  File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/local/lib/python2.7/site-packages/numba/errors.py", line 265, in new_error_context
    six.reraise(type(newerr), newerr, sys.exc_info()[2])
  File "/usr/local/lib/python2.7/site-packages/numba/errors.py", line 259, in new_error_context
    yield
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 216, in lower_block
    self.lower_inst(inst)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 305, in lower_inst
    return self.lower_setitem(inst.target, inst.index_var, inst.value, signature)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 390, in lower_setitem
    signature.args[2])
  File "/usr/local/lib/python2.7/site-packages/numba/targets/base.py", line 648, in cast
    "Cannot cast %s to %s: %s" % (fromty, toty, val))
LoweringError: Cannot cast none to float64: %".117" = load i8*, i8** %"$0.10"
File "<ipython-input-52-1ddc111374d6>", line 13
[1] During: lowering "result[0] = $0.10" at <ipython-input-52-1ddc111374d6> (13)

Failed at nopython (nopython mode backend)
Cannot cast none to float64: %".117" = load i8*, i8** %"$0.10"
File "<ipython-input-52-1ddc111374d6>", line 13
[1] During: lowering "result[0] = $0.10" at <ipython-input-52-1ddc111374d6> (13)
LoweringErrorTraceback (most recent call last)
<ipython-input-52-1ddc111374d6> in <module>()
     15     return LowLevelCallable(wrapped.ctypes)
     16 
---> 17 @jit_filter_function
     18 def fmin(values):
     19     result = np.inf
<ipython-input-52-1ddc111374d6> in jit_filter_function(filter_function)
      8     jitted_function = numba.jit(filter_function, nopython=True)
      9 
---> 10     @cfunc(intc(CPointer(float64), intp, CPointer(float64), voidptr))
     11     def wrapped(values_ptr, len_values, result, data):
     12         values = carray(values_ptr, (len_values,), dtype=float64)
/usr/local/lib/python2.7/site-packages/numba/decorators.pyc in wrapper(func)
    251         if cache:
    252             res.enable_caching()
--> 253         res.compile()
    254         return res
    255 
/usr/local/lib/python2.7/site-packages/numba/ccallback.pyc in compile(self)
     65             cres = self._cache.load_overload(self._sig, self._targetdescr.target_context)
     66             if cres is None:
---> 67                 cres = self._compile_uncached()
     68                 self._cache.save_overload(self._sig, cres)
     69             else:
/usr/local/lib/python2.7/site-packages/numba/ccallback.pyc in _compile_uncached(self)
     78 
     79         # Compile native function
---> 80         cres = self._compiler.compile(sig.args, sig.return_type)
     81         assert not cres.objectmode  # disabled by compiler above
     82         fndesc = cres.fndesc
/usr/local/lib/python2.7/site-packages/numba/dispatcher.pyc in compile(self, args, return_type)
     78                                       impl,
     79                                       args=args, return_type=return_type,
---> 80                                       flags=flags, locals=self.locals)
     81         # Check typing error if object mode is used
     82         if cres.typing_error is not None and not flags.enable_pyobject:
/usr/local/lib/python2.7/site-packages/numba/compiler.pyc in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library)
    761     pipeline = Pipeline(typingctx, targetctx, library,
    762                         args, return_type, flags, locals)
--> 763     return pipeline.compile_extra(func)
    764 
    765 
/usr/local/lib/python2.7/site-packages/numba/compiler.pyc in compile_extra(self, func)
    358         self.lifted = ()
    359         self.lifted_from = None
--> 360         return self._compile_bytecode()
    361 
    362     def compile_ir(self, func_ir, lifted=(), lifted_from=None):
/usr/local/lib/python2.7/site-packages/numba/compiler.pyc in _compile_bytecode(self)
    720         """
    721         assert self.func_ir is None
--> 722         return self._compile_core()
    723 
    724     def _compile_ir(self):
/usr/local/lib/python2.7/site-packages/numba/compiler.pyc in _compile_core(self)
    707 
    708         pm.finalize()
--> 709         res = pm.run(self.status)
    710         if res is not None:
    711             # Early pipeline completion
/usr/local/lib/python2.7/site-packages/numba/compiler.pyc in run(self, status)
    244                     # No more fallback pipelines?
    245                     if is_final_pipeline:
--> 246                         raise patched_exception
    247                     # Go to next fallback pipeline
    248                     else:
LoweringError: Caused By:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 238, in run
    stage()
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 644, in stage_nopython_backend
    self._backend(lowerfn, objectmode=False)
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 599, in _backend
    lowered = lowerfn()
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 586, in backend_nopython_mode
    self.flags)
  File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 882, in native_lowering_stage
    lower.lower()
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 135, in lower
    self.lower_normal_function(self.fndesc)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 176, in lower_normal_function
    entry_block_tail = self.lower_function_body()
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 201, in lower_function_body
    self.lower_block(block)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 216, in lower_block
    self.lower_inst(inst)
  File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/local/lib/python2.7/site-packages/numba/errors.py", line 265, in new_error_context
    six.reraise(type(newerr), newerr, sys.exc_info()[2])
  File "/usr/local/lib/python2.7/site-packages/numba/errors.py", line 259, in new_error_context
    yield
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 216, in lower_block
    self.lower_inst(inst)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 305, in lower_inst
    return self.lower_setitem(inst.target, inst.index_var, inst.value, signature)
  File "/usr/local/lib/python2.7/site-packages/numba/lowering.py", line 390, in lower_setitem
    signature.args[2])
  File "/usr/local/lib/python2.7/site-packages/numba/targets/base.py", line 648, in cast
    "Cannot cast %s to %s: %s" % (fromty, toty, val))
LoweringError: Cannot cast none to float64: %".117" = load i8*, i8** %"$0.10"
File "<ipython-input-52-1ddc111374d6>", line 13
[1] During: lowering "result[0] = $0.10" at <ipython-input-52-1ddc111374d6> (13)

Failed at nopython (nopython mode backend)
Cannot cast none to float64: %".117" = load i8*, i8** %"$0.10"
File "<ipython-input-52-1ddc111374d6>", line 13
[1] During: lowering "result[0] = $0.10" at <ipython-input-52-1ddc111374d6> (13)

ValueError: Invalid scipy.LowLevelCallable signature on Windows

Thanks a lot for posting these recipes. I am trying to get your jit_filter_function decorator to work, but I get the same error as in one of the comments on your blog post:

ValueError: Invalid scipy.LowLevelCallable signature "long (double *, longlong, double *, void *)". Expected one of: ['int (double *, intptr_t, double *, void *)', 'int (double *, npy_intp, double *, void *)', 'int (double *, long long, double *, void *)']

This is with Python 3.6 on Windows and

>>> numba.__version__
'0.35.0+10.g143f70e'
>>> scipy.__version__
'0.19.1'

I have tried to modify this line

llc-tools/llc/ndimage.py

Line 11 in 576d70c

@cfunc(intc(CPointer(float64), intp, CPointer(float64), voidptr))

in any way I could think of, but am unable to produce a signature that scipy.LowLevelCallable likes. What am I missing?

TypingError: got an unexpected keyword argument 'ddof' using jit_filter_function on Windows

Hello! First I'd like to say this decorator has been great to work with, really appreciate jit_filter_function. I'm running into an error that pops up when adding the 'ddof' argument to np.nanstd within the filter function.

This code runs without flaw

@jit_filter_function
def fstd(values):
    values[values == 0] = np.nan
    result = np.nanstd(values)
    return result
std = generic_filter(<2d_numpy_array>, fstd, footprint=np.ones((5, 5)))

However, adding the ddof argument like this

@jit_filter_function
def fstd(values):
    values[values == 0] = np.nan
    result = np.nanstd(values, ddof=1)
    return result
std = generic_filter(<2d_numpy_array>, fstd, footprint=np.ones((5, 5)))

Throws this:

Traceback (most recent call last):
  File "C:/Users/jbrown/AppData/Roaming/JetBrains/PyCharmCE2021.1/scratches/hr_class_master.py", line 301, in <module>
    main()
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\memory_profiler.py", line 1186, in wrapper
    val = prof(func)(*args, **kwargs)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\memory_profiler.py", line 759, in f
    return func(*args, **kwds)
  File "C:/Users/jbrown/AppData/Roaming/JetBrains/PyCharmCE2021.1/scratches/hr_class_master.py", line 149, in main
    def fstd(values):
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\llc\ndimage.py", line 48, in jit_filter_function
    def wrapped(values_ptr, len_values, result, data):
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\decorators.py", line 282, in wrapper
    res.compile()
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_lock.py", line 35, in _acquire_compile_lock
    return func(*args, **kwargs)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\ccallback.py", line 67, in compile
    cres = self._compile_uncached()
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\ccallback.py", line 81, in _compile_uncached
    return self._compiler.compile(sig.args, sig.return_type)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\dispatcher.py", line 129, in compile
    raise retval
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\dispatcher.py", line 139, in _compile_cached
    retval = self._compile_core(args, return_type)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\dispatcher.py", line 152, in _compile_core
    cres = compiler.compile_extra(self.targetdescr.typing_context,
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler.py", line 716, in compile_extra
    return pipeline.compile_extra(func)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler.py", line 452, in compile_extra
    return self._compile_bytecode()
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler.py", line 520, in _compile_bytecode
    return self._compile_core()
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler.py", line 499, in _compile_core
    raise e
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler.py", line 486, in _compile_core
    pm.run(self.state)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_machinery.py", line 368, in run
    raise patched_exception
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_machinery.py", line 356, in run
    self._runPass(idx, pass_inst, state)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_lock.py", line 35, in _acquire_compile_lock
    return func(*args, **kwargs)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_machinery.py", line 311, in _runPass
    mutated |= check(pss.run_pass, internal_state)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\compiler_machinery.py", line 273, in check
    mangled = func(compiler_state)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\typed_passes.py", line 105, in run_pass
    typemap, return_type, calltypes, errs = type_inference_stage(
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\typed_passes.py", line 83, in type_inference_stage
    errs = infer.propagate(raise_errors=raise_errors)
  File "C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\typeinfer.py", line 1086, in propagate
    raise errors[0]
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Failed in nopython mode pipeline (step: nopython frontend)
No implementation of function Function(<function nanstd at 0x000001BA5B414F70>) found for signature:
 
 >>> nanstd(array(float64, 1d, C), ddof=Literal[int](1))
 
There are 2 candidate implementations:
  - Of which 2 did not match due to:
  Overload in function 'np_nanstd': File: numba\np\arraymath.py: Line 1231.
    With argument(s): '(array(float64, 1d, C), ddof=int64)':
   Rejected as the implementation raised a specific error:
     TypingError: got an unexpected keyword argument 'ddof'
  raised from C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\numba\core\typing\templates.py:791

During: resolving callee type: Function(<function nanstd at 0x000001BA5B414F70>)
During: typing of call at C:/Users/jbrown/AppData/Roaming/JetBrains/PyCharmCE2021.1/scratches/hr_class_master.py (151)


File "hr_class_master.py", line 151:
    def fstd(values):
        <source elided>
        values[values == 0] = np.nan
        result = np.nanstd(values, ddof=1)
        ^

During: resolving callee type: type(CPUDispatcher(<function main.<locals>.fstd at 0x000001BA0DBF04C0>))
During: typing of call at C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\llc\ndimage.py (50)

During: resolving callee type: type(CPUDispatcher(<function main.<locals>.fstd at 0x000001BA0DBF04C0>))
During: typing of call at C:\Users\jbrown\AppData\Local\Programs\Python\Python38\lib\site-packages\llc\ndimage.py (50)


File "..\..\..\..\Local\Programs\Python\Python38\lib\site-packages\llc\ndimage.py", line 50:
    def wrapped(values_ptr, len_values, result, data):
        <source elided>
        values = carray(values_ptr, (len_values,), dtype=float64)
        result[0] = jitted_function(values)
        ^

Is this functionality to be added, or error with the code itself? I'm using Python 3.8 on Windows

Pass arguments to the LowLevelCallable

@cfunc(intc(CPointer(float64), intp, CPointer(float64), voidptr))
def function(values_ptr, len_values, result, data):
  ...
  weights = carray(data, (1,), double)[0]
  ...

weights = [0.6, 0.8, 0.4]
seq = ctypes.c_double * len(weights)
arr = seq(*weights)
ptr = ctypes.cast(ctypes.pointer(arr), ctypes.c_void_p)
ndi.generic_filter(image, LowLevelCallable(function.ctypes, ptr), footprint=footprint)

Source:
scipy doc

Add function for scipy.integrate.quad

Users of numerical integration don't have a nice lowlevelcallable interface with Numba right now. See:

See https://docs.scipy.org/doc/scipy/reference/ccallback.html

Add continuous integration using github actions

• testing
• releases

See https://github.com/napari/napari, https://github.com/napari/magicgui, and https://github.com/scikit-image/scikit-image for example configurations.

Improve our testing

In #11, @trhallam added some basic tests (🎉!). We can be more elaborate:

• ensure that running the function with a lowlevelcallable and a Python callable (the un-decorated function) gives the same results
• ensure that lowlevelcallable is faster than pure python
• ensure that providing input array as output gives the desired results (not sure yet whether this is technically possible from the SciPy side).