djsutherland/cyflann

A Cython interface to FLANN

cyflann's Issues

Travis setup

Might be nice. Have it build and upload conda packages (and pip wheels?) too.

consider versiontools

http://versiontools.readthedocs.org/en/latest/

Implement clustering functions

Add a test that FLANNExtension / etc works

Would help with making sure #18 makes sense.

use the c++ api directly

Why not? It'll avoid a layer of indirection and maybe be simpler.

Probably conflicts with #6, but might make #9 easier.

FLANNExtension shouldn't link to libflann_cpp when not necessary

Detect the language of the extension? Or just a keyword argument? Probably just a keyword argument.

Add a .pxd interface so other cython users can use it

Failed to install throuch pip or setup.py on OS X

Environment:

• OS X El Capitan 10.11.6
• Python: 2.7.11
• Numpy: 1.11.1
• Pip: 8.1.2
• FLANN: stable 1.8.4 (installed via Homebrew)

Could not install by either:

pip install cyflann

Or setup.py after checking out the code:

python setup.py install

Error message was:

...
cyflann/index.c:254:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
         ^
1 error generated.
error: command 'clang' failed with exit status 1

Travis: test system installs of flann

Homebrew on OSX, apt on Ubuntu.

Interface incompatability

It would probably be nice if cyflann were a drop-in replacement for pyflann, in case anyone other than py-sdm is ever going to want to use it.

allow specifying nonstandard flann location in installation

Need to set include_dirs and extra_link_args appropriately.

Also, should publish these variables so consumers (like py-sdm) know where to compile/link to as well.

nn_radius() returns no more than 32 neighbors

nn_radius only gives me 32 neighbors max. Despite max_nn=-1 or 1024 and also params.max_neighbors doesn't work?

FLANN_DEFAULT_PARAMETERS linkage on Windows

For some reason, MSVC doesn't get FLANN_DEFAULT_PARAMETERS out of the import lib, even though it's there and objdump /exports lists it and everything.

https://ci.appveyor.com/project/dougalsutherland/cyflann/build/1.0.49

Would be nice to use this so we can stop redefining the default parameters and actually use them from the library.

is all the linking grossness still needed?

Anaconda uses rpath properly now. Was that the only reason we needed it?

Compile to a single library file ?

Hi Dougal,

Thanks for doing this. I'm pretty new to Cython and my C/C++ is from 20 years ago. I'd ideally like to wrap the FLANN C++ code in Cython and then compile it all to a single .so / .pyd file. Is this possible or will there always be two libs (one Cython, one FLANN native) ?

Thanks

Ian

test error

$ python test_vs_pyflann.py 
Traceback (most recent call last):
  File "test_vs_pyflann.py", line 4, in <module>
    import cyflann
  File "/home/magnolia/cyflann/cyflann/__init__.py", line 1, in <module>
    from .index import FLANNParameters, FLANNIndex, set_distance_type
ImportError: /home/magnolia/cyflann/cyflann/index.so: undefined symbol: DEFAULT_FLANN_PARAMETERS

Implement nn(), nn_radius() functions

Handle random seeds appropriately

I currently only use the non-randomized functions so this doesn't matter, but still, should fix it.

pickling not working properly on VC9

Don't know what's up with this.

https://ci.appveyor.com/project/dougalsutherland/cyflann/build/1.0.53/job/yknjkaaxgh0jt8f7

OSX: better support for nonstandard install paths

Passing an absolute path to the library name doesn't seem to be doing it for me anymore; not sure if this is a change in newer OSX versions or if I just didn't test appropriately earlier. Should manually run install_name_tool to fix it after compilation; example.

FLANNIndex handling of _data pointer

Have to figure out how to handle the _data pointer appropriately.

publish location of flann for consumers to link against

So that e.g. py-sdm doesn't have to find flann itself, it just does library_dirs=[cyflann.get_library_dirs()] or whatever.

support types other than float32

compile flann with setup.py install?

Would it be possible to actually compile FLANN with this thing? So that pip install cyflann would work even if you didn't have flann installed. (Though you'd still need cmake, unless I wanted to really go crazy.)

Would probably need the option of linking to a system install of flann also, though.

doesn't compile with cython 0.20.*

Because of the struct/dict conversion issue discussed here and here.

Dunno of a workaround, other than (a) manually enumerating all the possible options or (b) disabling as_dict() / __repr__() (which uses it).

build issue on OSX

(From djsutherland/py-sdm#32)

I am using anaconda and set up an environment as described. When I run:

 pip install 'https://github.com/dougalsutherland/py-sdm/tarball/master#egg=sdm-0.1.0dev'

I get the following error:

 ImportError: The Cython extension requires cyflann to be installed before compilation.

 Install cyflann (e.g. `pip install cyflann`), and then try again.

I just ran pip install cyflann and it still raises this exception.

Running python -c 'import cyflann' gives me another error:

ImportError: dlopen(/Users/wgmueller/anaconda/envs/py-sdm2/lib/python2.7/site-packages/cyflann/index.so, 2): Symbol not found: _DEFAULT_FLANN_PARAMETERS
Referenced from: /Users/wgmueller/anaconda/envs/py-sdm2/lib/python2.7/site-packages/cyflann/index.so
Expected in: dynamic lookup

Any suggestions?