def resample(img, sub_rate=0.5):
"""
resample image based on the value of sub_rate.
the input image can be either 2D image or 3D volume.
sub_rate < 1.0, subsampling the image.
sub_rate > 1.0, upsampling the image using new gridding interpolation.
fit_to_fft will change the ouput image size to an fft_friendly size
"""
from fundamentals import subsample
from utilities import get_pixel_size, set_pixel_size
if type(img) == str:
from utilities import get_image
img = get_image(img)
nx = img.get_xsize()
ny = img.get_ysize()
nz = img.get_zsize()
if( ny == 1): ERROR("Only 2D or 3D images allowed","resample",1)
if sub_rate == 1.0: return img.copy()
elif sub_rate < 1.0:
e = subsample(img, sub_rate)
else: # sub_rate>1
new_nx = int(nx*sub_rate+0.5)
new_ny = int(ny*sub_rate+0.5)
if nz==1:
new_nz = 1
else:
new_nz = int(ny*sub_rate+0.5)
if ( nx!=ny and nz==1 ):
nn = max(new_nx, new_ny)
e = Util.pad(img, nn, nn, 1, 0, 0, 0, "circumference")
e, kb = prepi(e)
e = Util.window( e.rot_scale_conv_new(0.0, 0.0, 0.0, kb, sub_rate), new_nx, new_ny, 1, 0,0,0)
elif ((nx!=ny or nx!=nz or ny!=nz) and nz>1):
nn = max(new_nx, new_ny,new_nz)
e = Util.pad(img, nn, nn, nn, 0, 0, 0, "circumference")
e, kb = prepi3D(e)
e = Util.window( e.rot_scale_conv_new_3D(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, kb, sub_rate), new_nx, new_ny, new_nz, 0,0,0)
else:
if nz==1:
e, kb = prepi(Util.pad(img, new_nx, new_ny, 1, 0, 0, 0, "circumference"))
e = e.rot_scale_conv_new(0.0, 0.0, 0.0, kb, sub_rate)
else:
e, kb = prepi3D(Util.pad(img, new_nx, new_ny, new_nz, 0, 0, 0, "circumference"))
e = e.rot_scale_conv_new_3D(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, kb, sub_rate)
# Automatically adjust pixel size for ctf parameters
from utilities import get_pixel_size, set_pixel_size
apix = get_pixel_size(e)
apix /= sub_rate
set_pixel_size(e, apix)
return e
def fdownsample(img, sub_rate=0.5, RetReal = True):
"""
resample image based on the value of sub_rate.
the input image can be either 2D image or 3D volume.
sub_rate < 1.0, subsampling the image.
sub_rate > 1.0, upsampling the image using new gridding interpolation.
fit_to_fft will change the ouput image size to an fft_friendly size
"""
from fundamentals import fdecimate
from utilities import get_pixel_size, set_pixel_size
if type(img) == str:
from utilities import get_image
img = get_image(img)
nx = img.get_xsize()
if img.is_complex():
nx -= (2-nx%2)
ny = img.get_ysize()
nz = img.get_zsize()
if( ny == 1): ERROR("Only 2D or 3D images allowed","resample",1)
if sub_rate == 1.0: return img.copy()
elif sub_rate < 1.0:
nnx = int(nx*sub_rate+0.5)
nny = int(ny*sub_rate+0.5)
nnz = int(nz*sub_rate+0.5)
e = fdecimate(img, nnx, nny, nnz, RetReal = RetReal)
else: # sub_rate>1
ERROR("fdownsample","upscaling not implemented",1)
"""
new_nx = int(nx*sub_rate+0.5)
new_ny = int(ny*sub_rate+0.5)
if nz==1:
new_nz = 1
else:
new_nz = int(ny*sub_rate+0.5)
if ( nx!=ny and nz==1 ):
nn = max(new_nx, new_ny)
e = Util.pad(img, nn, nn, 1, 0, 0, 0, "circumference")
e, kb = prepi(e)
e = Util.window( e.rot_scale_conv_new(0.0, 0.0, 0.0, kb, sub_rate), new_nx, new_ny, 1, 0,0,0)
elif ((nx!=ny or nx!=nz or ny!=nz) and nz>1):
nn = max(new_nx, new_ny,new_nz)
e = Util.pad(img, nn, nn, nn, 0, 0, 0, "circumference")
e, kb = prepi3D(e)
e = Util.window( e.rot_scale_conv_new_3D(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, kb, sub_rate), new_nx, new_ny, new_nz, 0,0,0)
else:
if nz==1:
e, kb = prepi(Util.pad(img, new_nx, new_ny, 1, 0, 0, 0, "circumference"))
e = e.rot_scale_conv_new(0.0, 0.0, 0.0, kb, sub_rate)
else:
e, kb = prepi3D(Util.pad(img, new_nx, new_ny, new_nz, 0, 0, 0, "circumference"))
e = e.rot_scale_conv_new_3D(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, kb, sub_rate)
"""
# Automatically adjust pixel size for ctf parameters
from utilities import get_pixel_size, set_pixel_size
apix = get_pixel_size(e)
apix /= sub_rate
set_pixel_size(e, apix)
cc = e.get_attr_default("xform.projection", None)
if cc:
cp = cc.get_params("spider")
cp["tx"] *= sub_rate
cp["ty"] *= sub_rate
from utilities import set_params_proj
set_params_proj(e, [cp["phi"], cp["theta"], cp["psi"], -cp["tx"], -cp["ty"]]) # have to invert as set inverts them again
cc = e.get_attr_default("xform.align2d", None)
if cc:
cp = cc.get_params("2D")
cp["tx"] *= sub_rate
cp["ty"] *= sub_rate
from utilities import set_params2D
set_params2D(e, [cp["alpha"], cp["tx"], cp["ty"], cp["mirror"], cp["scale"]])
return e