def bilateral3(data, size_filter, sigma_p, sigma_x=10.):
"""bilateral filter """
dtype = data.dtype.type
dtypes_kernels = {
np.float32: "bilat3_float",
}
if not dtype in dtypes_kernels.keys():
logger.info("data type %s not supported yet (%s), casting to float:" %
(dtype, dtypes_kernels.keys()))
data = data.astype(np.float32)
dtype = data.dtype.type
img = OCLImage.from_array(data)
res = OCLArray.empty_like(data)
prog = OCLProgram(abspath("kernels/bilateral3.cl"))
print img.shape
prog.run_kernel(dtypes_kernels[dtype], img.shape, None, img, res.data,
np.int32(img.shape[0]), np.int32(img.shape[1]),
np.int32(size_filter), np.float32(sigma_x),
np.float32(sigma_p))
return res.get()
def bilateral3(data, size_filter, sigma_p, sigma_x = 10.):
"""bilateral filter """
dtype = data.dtype.type
dtypes_kernels = {np.float32:"bilat3_float",}
if not dtype in dtypes_kernels.keys():
logger.info("data type %s not supported yet (%s), casting to float:"%(dtype,dtypes_kernels.keys()))
data = data.astype(np.float32)
dtype = data.dtype.type
img = OCLImage.from_array(data)
res = OCLArray.empty_like(data)
prog = OCLProgram(abspath("kernels/bilateral3.cl"))
print img.shape
prog.run_kernel(dtypes_kernels[dtype],
img.shape,None,
img,res.data,
np.int32(img.shape[0]),np.int32(img.shape[1]),
np.int32(size_filter),np.float32(sigma_x),np.float32(sigma_p))
return res.get()
def scale(data, scale=(1., 1., 1.), interp="linear"):
"""returns a interpolated, scaled version of data
scale = (scale_z,scale_y,scale_x)
or
scale = scale_all
interp = "linear" | "nearest"
"""
bop = {"linear": "", "nearest": "-D USENEAREST"}
if not interp in bop.keys():
raise KeyError("interp = '%s' not defined ,valid: %s" %
(interp, bop.keys()))
if not isinstance(scale, (tuple, list, np.ndarray)):
scale = (scale, ) * 3
if len(scale) != 3:
raise ValueError("scale = %s misformed" % scale)
d_im = OCLImage.from_array(data)
nshape = np.array(data.shape) * np.array(scale)
nshape = tuple(nshape.astype(np.int))
res_g = OCLArray.empty(nshape, np.float32)
prog = OCLProgram(abspath("kernels/scale.cl"), build_options=[bop[interp]])
prog.run_kernel("scale", res_g.shape[::-1], None, d_im, res_g.data)
return res_g.get()
def nlm3(data, sigma, size_filter=2, size_search=3):
"""for noise level of sigma_0, choose sigma = 1.5*sigma_0
"""
prog = OCLProgram(abspath("kernels/nlm3.cl"),
build_options="-D FS=%i -D BS=%i" %
(size_filter, size_search))
img = OCLImage.from_array(data)
distImg = OCLImage.empty_like(data)
distImg = OCLImage.empty_like(data)
tmpImg = OCLImage.empty_like(data)
tmpImg2 = OCLImage.empty_like(data)
accBuf = OCLArray.zeros(data.shape, np.float32)
weightBuf = OCLArray.zeros(data.shape, np.float32)
for dx in range(size_search + 1):
for dy in range(-size_search, size_search + 1):
for dz in range(-size_search, size_search + 1):
prog.run_kernel("dist", img.shape, None, img, tmpImg,
np.int32(dx), np.int32(dy), np.int32(dz))
prog.run_kernel("convolve", img.shape, None, tmpImg, tmpImg2,
np.int32(1))
prog.run_kernel("convolve", img.shape, None, tmpImg2, tmpImg,
np.int32(2))
prog.run_kernel("convolve", img.shape, None, tmpImg, distImg,
np.int32(4))
prog.run_kernel("computePlus", img.shape, None, img, distImg,
accBuf.data, weightBuf.data,
np.int32(img.shape[0]), np.int32(img.shape[1]),
np.int32(img.shape[2]), np.int32(dx),
np.int32(dy), np.int32(dz), np.float32(sigma))
if any([dx, dy, dz]):
prog.run_kernel("computeMinus", img.shape, None, img,
distImg, accBuf.data, weightBuf.data,
np.int32(img.shape[0]),
np.int32(img.shape[1]),
np.int32(img.shape[2]), np.int32(dx),
np.int32(dy), np.float32(sigma))
acc = accBuf.get()
weights = weightBuf.get()
return acc / weights
def _convolve_sep2_gpu(data_g, hx_g, hy_g, res_g = None, dev = None):
assert_bufs_type(np.float32,data_g,hx_g,hy_g)
prog = OCLProgram(abspath("kernels/convolve_sep.cl"))
Ny,Nx = hy_g.shape[0],hx_g.shape[0]
tmp_g = OCLArray.empty_like(data_g)
if res_g is None:
res_g = OCLArray.empty_like(data_g)
prog.run_kernel("conv_sep2_x",data_g.shape[::-1],None,data_g.data,hx_g.data,tmp_g.data,np.int32(Nx))
prog.run_kernel("conv_sep2_y",data_g.shape[::-1],None,tmp_g.data,hy_g.data,res_g.data,np.int32(Ny))
return res_g
def _convolve_buf(data_g, h_g , res_g = None):
"""
buffer variant
"""
assert_bufs_type(np.float32,data_g,h_g)
prog = OCLProgram(abspath("kernels/convolve.cl"))
if res_g is None:
res_g = OCLArray.empty(data_g.shape,dtype=np.float32)
Nhs = [np.int32(n) for n in h_g.shape]
kernel_name = "convolve%sd_buf"%(len(data_g.shape))
prog.run_kernel(kernel_name,data_g.shape[::-1],None,
data_g.data,h_g.data,res_g.data,
*Nhs)
return res_g
def nlm2(data,sigma, size_filter = 2, size_search = 3):
"""for noise level of sigma_0, choose sigma = 1.5*sigma_0
"""
prog = OCLProgram(abspath("kernels/nlm2.cl"),
build_options="-D FS=%i -D BS=%i"%(size_filter,size_search))
img = OCLImage.from_array(data)
distImg = OCLImage.empty_like(data)
distImg = OCLImage.empty_like(data)
tmpImg = OCLImage.empty_like(data)
tmpImg2 = OCLImage.empty_like(data)
accBuf = OCLArray.zeros(data.shape,np.float32)
weightBuf = OCLArray.zeros(data.shape,np.float32)
for dx in range(size_search+1):
for dy in range(-size_search,size_search+1):
prog.run_kernel("dist",img.shape,None,
img,tmpImg,np.int32(dx),np.int32(dy))
prog.run_kernel("convolve",img.shape,None,
tmpImg,tmpImg2,np.int32(1))
prog.run_kernel("convolve",img.shape,None,
tmpImg2,distImg,np.int32(2))
prog.run_kernel("computePlus",img.shape,None,
img,distImg,accBuf.data,weightBuf.data,
np.int32(img.shape[0]),np.int32(img.shape[1]),
np.int32(dx),np.int32(dy),np.float32(sigma))
if any([dx,dy]):
prog.run_kernel("computeMinus",img.shape,None,
img,distImg,accBuf.data,weightBuf.data,
np.int32(img.shape[0]),np.int32(img.shape[1]),
np.int32(dx),np.int32(dy),np.float32(sigma))
acc = accBuf.get()
weights = weightBuf.get()
return acc/weights
def affine(data, mat = np.identity(4), interp = "linear"):
"""affine transform data with matrix mat
"""
bop = {"linear":"","nearest":"-D USENEAREST"}
if not interp in bop.keys():
raise KeyError("interp = '%s' not defined ,valid: %s"%(interp,bop.keys()))
d_im = OCLImage.from_array(data)
res_g = OCLArray.empty(data.shape,np.float32)
mat_g = OCLArray.from_array(np.linalg.inv(mat).astype(np.float32,copy=False))
prog = OCLProgram(abspath("kernels/transformations.cl")
, build_options=[bop[interp]])
prog.run_kernel("affine",
data.shape[::-1],None,
d_im,res_g.data,mat_g.data)
return res_g.get()
def affine(data, mat=np.identity(4), interp="linear"):
"""affine transform data with matrix mat
"""
bop = {"linear": "", "nearest": "-D USENEAREST"}
if not interp in bop.keys():
raise KeyError("interp = '%s' not defined ,valid: %s" %
(interp, bop.keys()))
d_im = OCLImage.from_array(data)
res_g = OCLArray.empty(data.shape, np.float32)
mat_g = OCLArray.from_array(
np.linalg.inv(mat).astype(np.float32, copy=False))
prog = OCLProgram(abspath("kernels/transformations.cl"),
build_options=[bop[interp]])
prog.run_kernel("affine", data.shape[::-1], None, d_im, res_g.data,
mat_g.data)
return res_g.get()
def _convolve3_old(data,h, dev = None):
"""convolves 3d data with kernel h on the GPU Device dev
boundary conditions are clamping to edge.
h is converted to float32
if dev == None the default one is used
"""
if dev is None:
dev = get_device()
if dev is None:
raise ValueError("no OpenCLDevice found...")
dtype = data.dtype.type
dtypes_options = {np.float32:"",
np.uint16:"-D SHORTTYPE"}
if not dtype in dtypes_options.keys():
raise TypeError("data type %s not supported yet, please convert to:"%dtype,dtypes_options.keys())
prog = OCLProgram(abspath("kernels/convolve3.cl"),
build_options = dtypes_options[dtype])
hbuf = OCLArray.from_array(h.astype(np.float32))
img = OCLImage.from_array(data)
res = OCLArray.empty(data.shape,dtype=np.float32)
Ns = [np.int32(n) for n in data.shape+h.shape]
prog.run_kernel("convolve3d",img.shape,None,
img,hbuf.data,res.data,
*Ns)
return res.get()
def scale(data, scale = (1.,1.,1.), interp = "linear"):
"""returns a interpolated, scaled version of data
scale = (scale_z,scale_y,scale_x)
or
scale = scale_all
interp = "linear" | "nearest"
"""
bop = {"linear":"","nearest":"-D USENEAREST"}
if not interp in bop.keys():
raise KeyError("interp = '%s' not defined ,valid: %s"%(interp,bop.keys()))
if not isinstance(scale,(tuple, list, np.ndarray)):
scale = (scale,)*3
if len(scale) != 3:
raise ValueError("scale = %s misformed"%scale)
d_im = OCLImage.from_array(data)
nshape = np.array(data.shape)*np.array(scale)
nshape = tuple(nshape.astype(np.int))
res_g = OCLArray.empty(nshape,np.float32)
prog = OCLProgram(abspath("kernels/scale.cl"), build_options=[bop[interp]])
prog.run_kernel("scale",
res_g.shape[::-1],None,
d_im,res_g.data)
return res_g.get()
from abspath import abspath
DEBUG = True
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', '*****@*****.**'),
)
MANAGERS = ADMINS
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.sqlite3', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
'NAME': abspath('database.db'), # Or path to database file if using sqlite3.
'USER': '', # Not used with sqlite3.
'PASSWORD': '', # Not used with sqlite3.
'HOST': '', # Set to empty string for localhost. Not used with sqlite3.
'PORT': '', # Set to empty string for default. Not used with sqlite3.
}
}
LOGIN_REDIRECT_URL = '/'
FLASH_IGNORE_MEDIA = True
FLASH_STORAGE = 'session'
FLASH_CODEC = 'json'
# Local time zone for this installation. Choices can be found here:
# http://en.wikipedia.org/wiki/List_of_tz_zones_by_name
from abspath import abspath
DEBUG = True
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', '*****@*****.**'),
)
MANAGERS = ADMINS
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.sqlite3', # Add 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
'NAME': abspath('database.db'), # Or path to database file if using sqlite3.
'USER': '', # Not used with sqlite3.
'PASSWORD': '', # Not used with sqlite3.
'HOST': '', # Set to empty string for localhost. Not used with sqlite3.
'PORT': '', # Set to empty string for default. Not used with sqlite3.
}
}
LOGIN_REDIRECT_URL = '/'
FLASH_IGNORE_MEDIA = True
FLASH_STORAGE = 'session'
FLASH_CODEC = 'json'
# Local time zone for this installation. Choices can be found here:
# http://en.wikipedia.org/wiki/List_of_tz_zones_by_name
from django.conf.urls.defaults import *
from django.shortcuts import redirect
from abspath import abspath
# Uncomment the next two lines to enable the admin:
from django.contrib import admin
admin.autodiscover()
urlpatterns = patterns('',
(r'^$', lambda req:redirect('/beanstalk/')),
(r'^beanstalk/', include('beanstalk.urls')),
(r'^accounts/login/$', 'django.contrib.auth.views.login',
{'template_name':'accounts/login.html'}),
(r'^accounts/logout/$', 'django.contrib.auth.views.logout_then_login'),
(r'^media/(?P<path>.*)$', 'django.views.static.serve',
{'document_root': abspath('media')}),
# Uncomment the next line to enable the admin:
(r'^admin/', include(admin.site.urls)),
)
# Django settings for jack project.
from abspath import abspath
DEBUG = True
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', '*****@*****.**'),
)
MANAGERS = ADMINS
DATABASE_ENGINE = 'sqlite3' # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'oracle'.
DATABASE_NAME = abspath(
'database.db') # Or path to database file if using sqlite3.
DATABASE_USER = '' # Not used with sqlite3.
DATABASE_PASSWORD = '' # Not used with sqlite3.
DATABASE_HOST = '' # Set to empty string for localhost. Not used with sqlite3.
DATABASE_PORT = '' # Set to empty string for default. Not used with sqlite3.
BEANSTALK_HOST = 'localhost'
BEANSTALK_PORT = 11300
LOGIN_REDIRECT_URL = '/'
FLASH_IGNORE_MEDIA = True
FLASH_STORAGE = 'session'
FLASH_CODEC = 'json'
# Local time zone for this installation. Choices can be found here:
from django.conf.urls.defaults import *
from django.shortcuts import redirect
from abspath import abspath
# Uncomment the next two lines to enable the admin:
from django.contrib import admin
admin.autodiscover()
urlpatterns = patterns(
'',
(r'^$', lambda req: redirect('/beanstalk/')),
(r'^beanstalk/', include('beanstalk.urls')),
(r'^accounts/login/$', 'django.contrib.auth.views.login', {
'template_name': 'accounts/login.html'
}),
(r'^accounts/logout/$', 'django.contrib.auth.views.logout_then_login'),
(r'^media/(?P<path>.*)$', 'django.views.static.serve', {
'document_root': abspath('media')
}),
# Uncomment the next line to enable the admin:
(r'^admin/', include(admin.site.urls)),
)
