Ejemplo n.º 1
0
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
Ejemplo n.º 2
0
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