Python loadCLibraryの例

コード例 #1

ファイル: homotopy_c.py プロジェクト: ymsigal/storm-analysis

def setCInterface(homotopy_lib):
    global homotopy

    homotopy = loadclib.loadCLibrary(os.path.dirname(__file__), homotopy_lib)

    l1flt_size = homotopy.getL1FLTSize()
    if (l1flt_size == 4):
        float_type = c_float
        float_array_type = numpy.float32
    elif (l1flt_size == 8):
        float_type = c_double
        float_array_type = numpy.float64

    homotopy.getXVector.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.initialize.argtypes = [
        ndpointer(dtype=float_array_type), c_int, c_int, c_int, c_int, c_int
    ]
    homotopy.l2Error.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.l2Error.restype = float_type
    homotopy.newYVector.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.solve.argtypes = [float_type, c_int]
    homotopy.solve.restype = float_type

    if (hasattr(homotopy, "getVisited")):
        homotopy.getVisited.argtypes = [ndpointer(dtype=numpy.int32)]

    if (hasattr(homotopy, "initializeGPU")):
        homotopy.initializeGPU.argtypes = [c_char_p, c_int, c_int, c_int]

コード例 #2

ファイル: homotopy_c.py プロジェクト: aaristov/storm-analysis

def setCInterface(homotopy_lib):
    global homotopy

    homotopy = loadclib.loadCLibrary(os.path.dirname(__file__), homotopy_lib)

    l1flt_size = homotopy.getL1FLTSize()
    if(l1flt_size == 4):
        float_type = c_float
        float_array_type = numpy.float32
    elif(l1flt_size == 8):
        float_type = c_double
        float_array_type = numpy.float64

    homotopy.getXVector.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.initialize.argtypes = [ndpointer(dtype=float_array_type),
                                    c_int,
                                    c_int,
                                    c_int,
                                    c_int,
                                    c_int]
    homotopy.l2Error.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.l2Error.restype = float_type
    homotopy.newYVector.argtypes = [ndpointer(dtype=float_array_type)]
    homotopy.solve.argtypes = [float_type, c_int]
    homotopy.solve.restype = float_type

    if(hasattr(homotopy, "getVisited")):
        homotopy.getVisited.argtypes = [ndpointer(dtype=numpy.int32)]

    if(hasattr(homotopy, "initializeGPU")):
        homotopy.initializeGPU.argtypes = [c_char_p,
                                           c_int,
                                           c_int,
                                           c_int]

コード例 #3

ファイル: rolling_ball_lib_c.py プロジェクト: linghumit/storm-analysis

#
# Hazen
#

import numpy
import os
import scipy
import scipy.ndimage

import ctypes
import numpy
from numpy.ctypeslib import ndpointer

import sa_library.loadclib as loadclib

rball = loadclib.loadCLibrary(os.path.dirname(__file__), "rolling_ball_lib")

# C interface definition
rball.estimateBg.argtypes = [
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64), ctypes.c_int, ctypes.c_int
]
rball.init.argtypes = [ndpointer(dtype=numpy.float64), ctypes.c_int]


class CRollingBall(object):
    def __init__(self, ball_radius, smoothing_sigma):
        self.ball_radius = ball_radius
        self.smoothing_sigma = smoothing_sigma

        ball_size = int(round(ball_radius * 0.5))

コード例 #4

ファイル: ia_utilities_c.py プロジェクト: aaristov/storm-analysis

#!/usr/bin/python
#
# Simple Python interface to utilities.c.
#
# Hazen 6/11
#

from ctypes import *
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

util = loadclib.loadCLibrary(os.path.dirname(__file__), "ia_utilities")

# C interface definition
util.findLocalMaxima.argtypes = [ndpointer(dtype=numpy.float64),
                                 ndpointer(dtype=numpy.int32),
                                 ndpointer(dtype=numpy.float64),
                                 c_double,
                                 c_double,
                                 c_double,
                                 c_double,
                                 c_int,
                                 c_int,
                                 c_int,
                                 c_int]
util.findLocalMaxima.restype = c_int
util.getBackgroundIndex.restype = c_int

コード例 #5

# Simple Python interface to grid.c. This is a somewhat faster
# but less flexible approach to creating 2D and 3D histograms
# than using the built-in numpy function numpy.histogramdd().
#
# Hazen 12/11
#

from ctypes import *
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

grid = loadclib.loadCLibrary(os.path.dirname(__file__), "grid")

# Function specifications
grid.grid2D.argtypes = [
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.int32), c_int, c_int, c_int
]

grid.grid3D.argtypes = [
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.int32), c_int, c_int, c_int, c_int
]

コード例 #6

#!/usr/bin/python
#
# Draws guassians onto a user supplied image.
#
# Hazen 01/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

drawgauss = loadclib.loadCLibrary(os.path.dirname(__file__), "draw_gaussians")

drawgauss.drawGaussians.argtypes = [
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64), ctypes.c_int, ctypes.c_int, ctypes.c_int,
    ctypes.c_int
]


def cDrawGaussians(image, objects, resolution):
    c_image = numpy.ascontiguousarray(image, dtype=numpy.float64)
    c_objects = numpy.ascontiguousarray(objects, dtype=numpy.float64)
    drawgauss.drawGaussians(c_image, c_objects, c_image.shape[1],
                            c_image.shape[0], objects.shape[0], resolution)
    return c_image

コード例 #7

ファイル: matched_filter_c.py プロジェクト: cmriddle/storm-analysis

#!/usr/bin/env python
#
# Simply Python interface to matched_filter.c
#
# Hazen 3/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os

import sa_library.loadclib as loadclib
import sa_library.recenter_psf as recenterPSF

m_filter = loadclib.loadCLibrary(os.path.dirname(__file__), "matched_filter")

m_filter.cleanup.argtypes = [ctypes.c_void_p]
m_filter.convolve.argtypes = [ctypes.c_void_p,
                              ndpointer(dtype = numpy.float64),
                              ndpointer(dtype = numpy.float64)]
m_filter.initialize.argtypes = [ndpointer(dtype = numpy.float64),
                                ctypes.c_int,
                                ctypes.c_int]
m_filter.initialize.restype = ctypes.c_void_p


class MatchedFilterException(Exception):

    def __init__(self, message):
        Exception.__init__(self, message)

コード例 #8

#        and cleanup once, rather than for every image in movie.
#        Also, all the static variables should be removed from
#        multi_fit.c
#

from ctypes import *
import math
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.ia_utilities_c as util_c
import sa_library.loadclib as loadclib

multi = loadclib.loadCLibrary(os.path.dirname(__file__), "multi_fit")

# C interface definition
multi.getError.restype = c_double
multi.getResidual.argtypes = [ndpointer(dtype=numpy.float64)]
multi.getResults.argtypes = [ndpointer(dtype=numpy.float64)]
multi.getUnconverged.restype = c_int
multi.initialize.argtypes = [ndpointer(dtype=numpy.float64),
                             ndpointer(dtype=numpy.float64),
                             ndpointer(dtype=numpy.float64),
                             c_double, 
                             c_int, 
                             c_int,
                             c_int,
                             c_int]
multi.initializeZParameters.argtypes = [ndpointer(dtype=numpy.float64), 

コード例 #9

#!/usr/bin/python
#
# Simple Python interface to fista_decon_utilities.c
#
# Hazen 1/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

fd_util = loadclib.loadCLibrary(os.path.dirname(__file__), "fista_decon_utilities")

# C interface definition
fd_util.label.argtypes = [ndpointer(dtype=numpy.float64),
                          ndpointer(dtype=numpy.int32),
                          ctypes.c_double,
                          ctypes.c_int,
                          ctypes.c_int,
                          ctypes.c_int]
fd_util.label.restype = ctypes.c_int
fd_util.moments.argtypes = [ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.int32),
                            ctypes.c_int,
                            ctypes.c_int,
                            ctypes.c_int,

コード例 #10

ファイル: fista_fft_c.py プロジェクト: cmriddle/storm-analysis

# Simple Python interface to fista_fft.c
#
# Hazen 2/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

import fista_3d as fista3D

fista_fft = loadclib.loadCLibrary(os.path.dirname(__file__), "fista_fft")

# C interface definition
fista_fft.getXVector.argtypes = [ndpointer(dtype=numpy.float64)]
fista_fft.initialize2D.argtypes = [ndpointer(dtype=numpy.float64),
                                   ctypes.c_double,
                                   ctypes.c_int]
fista_fft.initialize3D.argtypes = [ndpointer(dtype=numpy.float64),
                                   ctypes.c_double,
                                   ctypes.c_int,
                                   ctypes.c_int]
fista_fft.iterate.argtypes = [ctypes.c_double]
fista_fft.l1Error.restype = ctypes.c_double
fista_fft.l2Error.restype = ctypes.c_double
fista_fft.newImage.argtypes = [ndpointer(dtype=numpy.float64)]
fista_fft.run.argtypes = [ctypes.c_double,

コード例 #11

ファイル: matched_filter_c.py プロジェクト: linghumit/storm-analysis

#!/usr/bin/env python
#
# Simply Python interface to matched_filter.c
#
# Hazen 3/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os

import sa_library.loadclib as loadclib
import sa_library.recenter_psf as recenterPSF

m_filter = loadclib.loadCLibrary(os.path.dirname(__file__), "matched_filter")

m_filter.cleanup.argtypes = [ctypes.c_void_p]
m_filter.convolve.argtypes = [
    ctypes.c_void_p,
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64)
]
m_filter.initialize.argtypes = [
    ndpointer(dtype=numpy.float64), ctypes.c_int, ctypes.c_int
]
m_filter.initialize.restype = ctypes.c_void_p


class MatchedFilterException(Exception):
    def __init__(self, message):

コード例 #12

ファイル: drawgaussians.py プロジェクト: cmriddle/storm-analysis

#!/usr/bin/python
#
# Draws guassians onto a user supplied image.
#
# Hazen 01/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

drawgauss = loadclib.loadCLibrary(os.path.dirname(__file__), "draw_gaussians")

drawgauss.drawGaussians.argtypes = [ndpointer(dtype = numpy.float64),
                                    ndpointer(dtype = numpy.float64),
                                    ctypes.c_int,
                                    ctypes.c_int,
                                    ctypes.c_int,
                                    ctypes.c_int]

def cDrawGaussians(image, objects, resolution):
    c_image = numpy.ascontiguousarray(image, dtype = numpy.float64)
    c_objects = numpy.ascontiguousarray(objects, dtype = numpy.float64)
    drawgauss.drawGaussians(c_image,
                            c_objects,
                            c_image.shape[1],
                            c_image.shape[0],

コード例 #13

ファイル: multi_fit_c.py プロジェクト: aaristov/storm-analysis

#
# Hazen
#
# 

from ctypes import *
import math
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.ia_utilities_c as util_c
import sa_library.loadclib as loadclib

multi = loadclib.loadCLibrary(os.path.dirname(__file__), "multi_fit")

# C interface definition
multi.getError.restype = c_double
multi.getResidual.argtypes = [ndpointer(dtype=numpy.float64)]
multi.getResults.argtypes = [ndpointer(dtype=numpy.float64)]
multi.getUnconverged.restype = c_int
multi.initialize.argtypes = [ndpointer(dtype=numpy.float64),
                             ndpointer(dtype=numpy.float64),
                             ndpointer(dtype=numpy.float64),
                             c_double, 
                             c_int, 
                             c_int,
                             c_int,
                             c_int]
multi.initializeZParameters.argtypes = [ndpointer(dtype=numpy.float64), 

コード例 #14

ファイル: scmos_utilities_c.py プロジェクト: aaristov/storm-analysis

# "Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms"
# F. Huang et al. Nature Methods, 10, p653-658.
#
# Hazen 10/13
#

import ctypes
import math
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

slib = loadclib.loadCLibrary(os.path.dirname(__file__), "scmos_utilities")

# C interface definition.
slib.deregularize.argtypes = [ndpointer(dtype=numpy.float64),
                              ndpointer(dtype=numpy.float64),
                              ndpointer(dtype=numpy.float64),
                              ndpointer(dtype=numpy.float64),
                              ndpointer(dtype=numpy.float64),
                              ctypes.c_int]

slib.regularize.argtypes = [ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.float64),
                            ndpointer(dtype=numpy.float64),
                            ctypes.c_int]

コード例 #15

ファイル: ia_utilities_c.py プロジェクト: linghumit/storm-analysis

#!/usr/bin/python
#
# Simple Python interface to utilities.c.
#
# Hazen 6/11
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

util = loadclib.loadCLibrary(os.path.dirname(__file__), "ia_utilities")

# C interface definition
util.findLocalMaxima.argtypes = [
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.int32),
    ndpointer(dtype=numpy.float64), ctypes.c_double, ctypes.c_double,
    ctypes.c_int, ctypes.c_int, ctypes.c_int, ctypes.c_int
]
util.findLocalMaxima.restype = ctypes.c_int
util.getBackgroundIndex.restype = ctypes.c_int
util.getErrorIndex.restype = ctypes.c_int
util.getHeightIndex.restype = ctypes.c_int
util.getNPeakPar.restype = ctypes.c_int
util.getNResultsPar.restype = ctypes.c_int
util.getStatusIndex.restype = ctypes.c_int

コード例 #16

# Simple Python interface to fista_fft.c
#
# Hazen 2/16
#

import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

import fista_3d as fista3D

fista_fft = loadclib.loadCLibrary(os.path.dirname(__file__), "fista_fft")

# C interface definition
fista_fft.getXVector.argtypes = [ndpointer(dtype=numpy.float64)]
fista_fft.initialize2D.argtypes = [
    ndpointer(dtype=numpy.float64), ctypes.c_double, ctypes.c_int
]
fista_fft.initialize3D.argtypes = [
    ndpointer(dtype=numpy.float64), ctypes.c_double, ctypes.c_int, ctypes.c_int
]
fista_fft.iterate.argtypes = [ctypes.c_double]
fista_fft.l1Error.restype = ctypes.c_double
fista_fft.l2Error.restype = ctypes.c_double
fista_fft.newImage.argtypes = [ndpointer(dtype=numpy.float64)]
fista_fft.run.argtypes = [ctypes.c_double, ctypes.c_int]

コード例 #17

ファイル: grid_c.py プロジェクト: aaristov/storm-analysis

# Simple Python interface to grid.c. This is a somewhat faster
# but less flexible approach to creating 2D and 3D histograms
# than using the built-in numpy function numpy.histogramdd().
#
# Hazen 12/11
#

from ctypes import *
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

grid = loadclib.loadCLibrary(os.path.dirname(__file__), "grid")

# Function specifications
grid.grid2D.argtypes = [ndpointer(dtype=numpy.int32),
                        ndpointer(dtype=numpy.int32),
                        ndpointer(dtype=numpy.int32),
                        c_int,
                        c_int,
                        c_int]

grid.grid3D.argtypes = [ndpointer(dtype=numpy.int32),
                        ndpointer(dtype=numpy.int32),
                        ndpointer(dtype=numpy.int32),
                        ndpointer(dtype=numpy.int32),
                        c_int,
                        c_int,

コード例 #18

# "Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms"
# F. Huang et al. Nature Methods, 10, p653-658.
#
# Hazen 10/13
#

import ctypes
import math
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys

import sa_library.loadclib as loadclib

slib = loadclib.loadCLibrary(os.path.dirname(__file__), "scmos_utilities")

# C interface definition.
slib.deregularize.argtypes = [
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64), ctypes.c_int
]

slib.regularize.argtypes = [
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),
    ndpointer(dtype=numpy.float64),