revert safe_division for sparx

sparx/bin/sx3dvariability.py

@@ -30,7 +30,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
 #
 #
-from past.utils import old_div
 from builtins import range
 from EMAN2 import *
 from sparx import *
@@ -243,7 +242,7 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 			img  = get_image(stack, 0)
 			nx   = img.get_xsize()
 			ny   = img.get_ysize()
-			if(min(nx, ny) < options.window):   keepgoing = 0
+			if int(options.decimate*min(nx, ny)+0.5)< options.window:keepgoing = 0
 		keepgoing = bcast_number_to_all(keepgoing, main_node, MPI_COMM_WORLD)
 		if keepgoing == 0: ERROR("The target window size cannot be larger than the size of decimated image", "sx3dvariability", 1, myid)
 
@@ -311,9 +310,9 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 					ERROR("Input stack is not prepared for symmetry, please follow instructions", "sx3dvariability", 1, myid)
 				from utilities import get_symt
 				i = len(get_symt(options.sym))
-				if((old_div(nima,i))*i != nima):
+				if((nima/i)*i != nima):
 					ERROR("The length of the input stack is incorrect for symmetry processing", "sx3dvariability", 1, myid)
-				symbaselen = old_div(nima,i)
+				symbaselen = nima/i
 			else:  symbaselen = nima
 		else:
 			nima = 0
@@ -336,14 +335,14 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 				nx = int(nx*options.decimate+0.5)
 				ny = int(ny*options.decimate+0.5)
 			else:
-				nx = int(options.window*options.decimate+0.5)
+				nx = int(options.window*decimate+0.5)
 				ny = nx
 		Tracker["nx"]  = nx
 		Tracker["ny"]  = ny
 		Tracker["nz"]  = nx
-
+		
 		symbaselen     = bcast_number_to_all(symbaselen)
-		if radiuspca == -1: radiuspca = old_div(nx,2)-2
+		if radiuspca == -1: radiuspca = nx/2-2
 
 		if myid == main_node: log_main.add("%-70s:  %d\n"%("Number of projection", nima))
 		img_begin, img_end = MPI_start_end(nima, number_of_proc, myid)
@@ -455,7 +454,7 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 				log_main.add("%-70s:  %.2f\n"%("Finding neighboring projections lasted [s]", time()-t2))
 				log_main.add("%-70s:  %d\n"%("Number of groups processed on the main node", len(proj_list)))
 				if options.VERBOSE:
-					log_main.add("Grouping projections took: ", old_div((time()-t2),60)	, "[min]")
+					log_main.add("Grouping projections took: ", (time()-t2)/60	, "[min]")
 					log_main.add("Number of groups on main node: ", len(proj_list))
 			mpi_barrier(MPI_COMM_WORLD)
 
@@ -529,7 +528,7 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 
 				if not options.no_norm:
 					#print grp_imgdata[j].get_xsize()
-					mask = model_circle(old_div(nx,2)-2, nx, nx)
+					mask = model_circle(nx/2-2, nx, nx)
 					for k in range(img_per_grp):
 						ave, std, minn, maxx = Util.infomask(grp_imgdata[k], mask, False)
 						grp_imgdata[k] -= ave
@@ -582,7 +581,7 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 
 				var = model_blank(nx,ny)
 				for q in grp_imgdata:  Util.add_img2( var, q )
-				Util.mul_scalar( var, old_div(1.0,(len(grp_imgdata)-1)))
+				Util.mul_scalar( var, 1.0/(len(grp_imgdata)-1))
 				# Switch to std dev
 				var = square_root(threshold(var))
 				#if options.CTF:	ave, var = avgvar_ctf(grp_imgdata, mode="a")
@@ -749,7 +748,7 @@ def params_3D_2D_NEW(phi, theta, psi, s2x, s2y, mirror):
 			if myid == main_node:
 				from fundamentals import fpol
 				res = fpol(res, int(org_nx*options.decimate+0.5),  int(org_ny*options.decimate+0.5),  int(org_nz*options.decimate+0.5))
-				res	= resample(res, old_div(1.,options.decimate))
+				res	= resample(res, 1./options.decimate)
 				set_pixel_size(res, 1.0)
 				res.write_image(os.path.join(options.output_dir, options.var3D))
 				log_main.add("%-70s:  %.2f\n"%("Reconstructing 3D variability took [s]", time()-t6))

sparx/bin/sxcenter_projections.py

@@ -33,7 +33,6 @@
 
 
 from __future__ import print_function
-from past.utils import old_div
 from builtins import range
 from builtins import object
 from EMAN2 import *
@@ -64,7 +63,7 @@ def fuselowf(vs, fq):
 	a = vs[0].copy()
 	for i in range(1,n):
 		Util.add_img(a, vs[i])
-	Util.mul_scalar(a, old_div(1.0,float(n)))
+	Util.mul_scalar(a, 1.0/float(n))
 	a = filt_tophatl(a, fq)
 	for i in range(n):
 		vs[i] = fft(Util.addn_img(a, filt_tophath(vs[i], fq)))
@@ -187,8 +186,8 @@ def run3Dalignment(paramsdict, partids, partstack, outputdir, procid, myid, main
 	ali3d_options.ts     = paramsdict["ts"]
 	ali3d_options.xr     = paramsdict["xr"]
 	#  low pass filter is applied to shrank data, so it has to be adjusted
-	ali3d_options.fl     = old_div(paramsdict["lowpass"],paramsdict["shrink"])
-	ali3d_options.initfl = old_div(paramsdict["initialfl"],paramsdict["shrink"])
+	ali3d_options.fl     = paramsdict["lowpass"]/paramsdict["shrink"]
+	ali3d_options.initfl = paramsdict["initialfl"]/paramsdict["shrink"]
 	ali3d_options.aa     = paramsdict["falloff"]
 	ali3d_options.maxit  = paramsdict["maxit"]
 	ali3d_options.mask3D = paramsdict["mask3D"]
@@ -199,7 +198,7 @@ def run3Dalignment(paramsdict, partids, partstack, outputdir, procid, myid, main
 	projdata = getindexdata(paramsdict["stack"], partids, partstack, myid, nproc)
 	onx = projdata[0].get_xsize()
 	last_ring = ali3d_options.ou
-	if last_ring < 0:	last_ring = int(old_div(onx,2)) - 2
+	if last_ring < 0:	last_ring = int(onx/2) - 2
 	mask2D  = model_circle(last_ring,onx,onx) - model_circle(ali3d_options.ir,onx,onx)
 	if(shrinkage < 1.0):
 		# get the new size
@@ -274,8 +273,8 @@ def run3Dalignment(paramsdict, partids, partstack, outputdir, procid, myid, main
 	#  store params
 	if(myid == main_node):
 		for im in range(nima):
-			params[im][0] = old_div(params[im][0],shrinkage) +oldshifts[im][0]
-			params[im][1] = old_div(params[im][1],shrinkage) +oldshifts[im][1]
+			params[im][0] = params[im][0]/shrinkage +oldshifts[im][0]
+			params[im][1] = params[im][1]/shrinkage +oldshifts[im][1]
 		line = strftime("%Y-%m-%d_%H:%M:%S", localtime()) + " =>"
 		print(line,"Executed successfully: ","3D alignment","  number of images:%7d"%len(params))
 		write_text_row(params, os.path.join(outputdir,"params.txt") )
@@ -381,11 +380,11 @@ def main():
 		if ali3d_options.CTF:
 			i = a.get_attr('ctf')
 			pixel_size = i.apix
-			fq = old_div(pixel_size,fq)
+			fq = pixel_size/fq
 		else:
 			pixel_size = 1.0
 			#  No pixel size, fusing computed as 5 Fourier pixels
-			fq = old_div(5.0,nxinit)
+			fq = 5.0/nxinit
 		del a
 	else:
 		total_stack = 0
@@ -437,7 +436,7 @@ def main():
 	else:  yr = options.yr
 
 	delta = float(options.delta)
-	if(delta <= 0.0):  delta = "%f"%round(degrees(atan(old_div(1.0,float(radi)))), 2)
+	if(delta <= 0.0):  delta = "%f"%round(degrees(atan(1.0/float(radi))), 2)
 	else:    delta = "%f"%delta
 
 	paramsdict = {	"stack":stack,"delta":delta, "ts":"1.0", "xr":xr, "an":angular_neighborhood, \

sparx/bin/sxchains.py

@@ -32,7 +32,6 @@
 #
 #
 
-from past.utils import old_div
 from builtins import range
 import	global_def
 from	global_def 	import *
@@ -63,7 +62,7 @@ def TotalDistance(city, lccc):
 
 def reverse(city, n):
     nct = len(city)
-    nn = old_div((1+ ((n[1]-n[0]) % nct)),2) # half the lenght of the segment to be reversed
+    nn = (1+ ((n[1]-n[0]) % nct))/2 # half the lenght of the segment to be reversed
     # the segment is reversed in the following way n[0]<->n[1], n[0]+1<->n[1]-1, n[0]+2<->n[1]-2,...
     # Start at the ends of the segment and swap pairs of cities, moving towards the center.
     for j in range(nn):
@@ -101,7 +100,7 @@ def tsp(lccc):
 
 	#     ncity = 100        # Number of cities to visit
 	from math import sqrt
-	ncity = int( old_div((1+sqrt(1+8*len(lccc))),2) )        # Number of cities to visit
+	ncity = int( (1+sqrt(1+8*len(lccc)))/2 )        # Number of cities to visit
     #  sanity check
 	if( ncity*(ncity-1)/2 != len(lccc) ): return [-1]
 
@@ -153,7 +152,7 @@ def tsp(lccc):
 				de = Distance(city[n[2]], city[n[1]], lccc) + Distance(city[n[3]], city[n[0]], lccc)\
 					 - Distance(city[n[2]], city[n[0]], lccc) - Distance(city[n[3]] ,city[n[1]], lccc)
 
-				if de<0 or exp(old_div(-de,T))>random.rand(): # Metropolis
+				if de<0 or exp(-de/T)>random.rand(): # Metropolis
 					accepted += 1
 					dist += de
 					reverse(city, n)
@@ -169,7 +168,7 @@ def tsp(lccc):
 				de += Distance( city[n[0]], city[n[4]], lccc) + Distance( city[n[1]], city[n[5]], lccc) \
 						+ Distance( city[n[2]], city[n[3]], lccc)
 
-				if de<0 or exp(old_div(-de,T))>random.rand(): # Metropolis
+				if de<0 or exp(-de/T)>random.rand(): # Metropolis
 					accepted += 1
 					dist += de
 					city = transpt(city, n)

sparx/bin/sxcompute_isac_avg.py

@@ -5,7 +5,6 @@
 #  New version of sort3D.
 #  
 from __future__ import print_function
-from past.utils import old_div
 from builtins import range
 import  os
 import  sys
@@ -101,22 +100,22 @@ def adjust_pw_to_model(image, pixel_size, roo):
 	c2 = 15.0
 	c3 = 0.2
 	c4 = -1.0
-	c5 = old_div(1.,5.)
+	c5 = 1./5.
 	c6 = 0.25 # six params are fitted to Yifan channel model
 	rot1 = rops_table(image)
 	fil  = [None]*len(rot1)
 	if roo is None: # adjusted to the analytic model, See Penczek Methods Enzymol 2010
 		pu = []
 		for ifreq in range(len(rot1)):
 			x = float(ifreq)/float(len(rot1))/pixel_size
-			v = exp(c1+old_div(c2,(old_div(x,c3)+1)**2)) + exp(c4-0.5*((old_div((x-c5),c6**2))**2))
+			v = exp(c1+c2/(x/c3+1)**2) + exp(c4-0.5*(((x-c5)/c6**2)**2))
 			pu.append(v)
 		s =sum(pu)
-		for ifreq in range(len(rot1)): fil[ifreq] = sqrt(old_div(pu[ifreq],(rot1[ifreq]*s)))
+		for ifreq in range(len(rot1)): fil[ifreq] = sqrt(pu[ifreq]/(rot1[ifreq]*s))
 	else: # adjusted to a given 1-d rotational averaged pw2
 		if roo[0]<0.1 or roo[0]>1.: s =sum(roo)
 		else:  s=1.0
-		for ifreq in range(len(rot1)):fil[ifreq] = sqrt(old_div(roo[ifreq],(rot1[ifreq]*s)))
+		for ifreq in range(len(rot1)):fil[ifreq] = sqrt(roo[ifreq]/(rot1[ifreq]*s))
 	return filt_table(image, fil)
 
 def get_optimistic_res(frc):
@@ -134,13 +133,13 @@ def get_optimistic_res(frc):
 
 def apply_enhancement(avg, B_start, pixel_size, user_defined_Bfactor):
 	guinierline = rot_avg_table(power(periodogram(avg),.5))
-	freq_max   =  old_div(1.,(2.*pixel_size))
-	freq_min   =  old_div(1.,B_start)
+	freq_max   =  1./(2.*pixel_size)
+	freq_min   =  1./B_start
 	b, junk, ifreqmin, ifreqmax = compute_bfactor(guinierline, freq_min, freq_max, pixel_size)
 	print(ifreqmin, ifreqmax)
 	global_b = b*4. #
 	if user_defined_Bfactor < 0.0: global_b = user_defined_Bfactor
-	sigma_of_inverse = sqrt(old_div(2.,global_b))
+	sigma_of_inverse = sqrt(2./global_b)
 	avg = filt_gaussinv(fft(avg), sigma_of_inverse)
 	return avg, global_b
 
@@ -338,7 +337,7 @@ def main():
 	Tracker = wrap_mpi_bcast(Tracker, Blockdata["main_node"], communicator = MPI_COMM_WORLD)
 
 	#print(Tracker["constants"]["pixel_size"], "pixel_size")	
-	x_range = max(Tracker["constants"]["xrange"], int(old_div(1.,Tracker["ini_shrink"]))+1)
+	x_range = max(Tracker["constants"]["xrange"], int(1./Tracker["ini_shrink"])+1)
 	y_range =  x_range
 
 	if(Blockdata["myid"] == Blockdata["main_node"]): parameters = read_text_row(os.path.join(Tracker["constants"]["isac_dir"], "all_parameters.txt"))
@@ -363,7 +362,7 @@ def main():
 				abs_id =  members[im]
 				global_dict[abs_id] = [iavg, im]
 				P = combine_params2( init_dict[abs_id][0], init_dict[abs_id][1], init_dict[abs_id][2], init_dict[abs_id][3], \
-				parameters[abs_id][0], old_div(parameters[abs_id][1],Tracker["ini_shrink"]), old_div(parameters[abs_id][2],Tracker["ini_shrink"]), parameters[abs_id][3])
+				parameters[abs_id][0], parameters[abs_id][1]/Tracker["ini_shrink"], parameters[abs_id][2]/Tracker["ini_shrink"], parameters[abs_id][3])
 				if parameters[abs_id][3] ==-1: 
 					print("WARNING: Image #{0} is an unaccounted particle with invalid 2D alignment parameters and should not be the member of any classes. Please check the consitency of input dataset.".format(abs_id)) # How to check what is wrong about mirror = -1 (Toshio 2018/01/11)
 				params_of_this_average.append([P[0], P[1], P[2], P[3], 1.0])

sparx/bin/sxconsistency.py

@@ -33,7 +33,6 @@
 
 #  VERSION 2  09/25/2014
 
-from past.utils import old_div
 from builtins import range
 from   EMAN2 import *
 from   sparx import *
@@ -93,13 +92,13 @@ def average2dtransform(data, return_avg_pixel_error=False):
 
 	# Get ave transform params
 	H = Transform({"type":"2D"})
-	H.set_matrix([old_div(sum_cosa,sqrtP), old_div(sum_sina,sqrtP), 0.0, sx, old_div(-sum_sina,sqrtP), old_div(sum_cosa,sqrtP), 0.0, sy, 0.0, 0.0, 1.0, 0.0])
+	H.set_matrix([sum_cosa/sqrtP, sum_sina/sqrtP, 0.0, sx, -sum_sina/sqrtP, sum_cosa/sqrtP, 0.0, sy, 0.0, 0.0, 1.0, 0.0])
 	dd = H.get_params("2D")
 
 	H = Transform({"type":"2D","alpha":dd[ "alpha" ],"tx":dd[ "tx" ],"ty": dd[ "ty" ],"mirror":0,"scale":1.0})
 	dd = H.get_params("2D")
 	if return_avg_pixel_error:
-		return old_div(sum(sqr_pixel_error),N)
+		return sum(sqr_pixel_error)/N
 	else:
 		return [dd[ "alpha" ], dd[ "tx" ], dd[ "ty" ]]
 
@@ -300,7 +299,7 @@ def average_trans(params):
 			nphi   = 0.0
 			ntheta = 0.0
 		else:
-			ntheta = degrees(acos(old_div(nas[2],nom)))%360.0
+			ntheta = degrees(acos(nas[2]/nom))%360.0
 			if(sym>1 and ntheta>90.0):  nphi   = (degrees(atan2( nas[1], nas[0] ))-180.0)%qsym + 180.0
 			else:                       nphi   =  degrees(atan2( nas[1], nas[0] ))%qsym
 
@@ -397,7 +396,7 @@ def main():
 					#print  ll,rw[0][j], rw[2][j]
 					break
 			if isame: thesame += 1
-		qt = old_div(float(thesame),nn)
+		qt = float(thesame)/nn
 		print("Proportion of the same orientations ",qt)
 		write_text_file([qt], os.path.join(outdir,howmanythesame) )
 
@@ -408,7 +407,7 @@ def main():
 		radius = options.ou
 		thresherr = options.thresherr  #for chc5 1, for ribo 4#4.0
 		sym = int(options.sym[1:])
-		qsym = old_div(360.0,sym)
+		qsym = 360.0/sym
 
 		blocks = ['A','B','C','D']
 		params = {}
@@ -487,7 +486,7 @@ def main():
 					nphi   = 0.0
 					ntheta = 0.0
 				else:
-					ntheta = degrees(acos(old_div(nas[2],nom)))%360.0
+					ntheta = degrees(acos(nas[2]/nom))%360.0
 					if(sym>1 and ntheta>90.0):  nphi   = (degrees(atan2( nas[1], nas[0] ))-180.0)%qsym + 180.0
 					else:                       nphi   = degrees(atan2( nas[1], nas[0] ))%qsym
 
@@ -619,7 +618,7 @@ def main():
 		radius = options.ou
 		thresherr = options.thresherr
 		sym = int(options.sym[1:])
-		qsym = old_div(360.0,sym)
+		qsym = 360.0/sym
 		#params = [[None for i in xrange(3)] for j in xrange(4)]
 		ll = 3 # this is hardwired as we have three groups.  however, I would like to keep the code general.
 		for jj in range(4):
@@ -671,7 +670,7 @@ def main():
 					nphi   = 0.0
 					ntheta = 0.0
 				else:
-					ntheta = degrees(acos(old_div(nas[2],nom)))%360.0
+					ntheta = degrees(acos(nas[2]/nom))%360.0
 					if(sym>1 and ntheta>90.0):  nphi   = (degrees(atan2( nas[1], nas[0] ))-180.0)%qsym + 180.0
 					else:                       nphi   =  degrees(atan2( nas[1], nas[0] ))%qsym
 
@@ -709,7 +708,7 @@ def main():
 		radius = options.ou
 		thresherr = options.thresherr
 		sym = int(options.sym[1:])
-		qsym = old_div(360.0,sym)
+		qsym = 360.0/sym
 		#params = [[None for i in xrange(3)] for j in xrange(4)]
 		ll = 3 # this is hardwired as we have three groups.  however, I would like to keep the code general.
 		for jj in range(1):
@@ -762,7 +761,7 @@ def main():
 					nphi   = 0.0
 					ntheta = 0.0
 				else:
-					ntheta = degrees(acos(old_div(nas[2],nom)))%360.0
+					ntheta = degrees(acos(nas[2]/nom))%360.0
 					if(sym>1 and ntheta>90.0):  nphi   = (degrees(atan2( nas[1], nas[0] ))-180.0)%qsym + 180.0
 					else:                       nphi   =  degrees(atan2( nas[1], nas[0] ))%qsym
 

sparx/bin/sxcter.py

@@ -31,7 +31,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
 #
 #
-from past.utils import old_div
 import os
 import sys
 from optparse import OptionParser
@@ -162,11 +161,11 @@ def main():
 
 	if options.f_start >0.0: 
 		if options.f_start <=0.5: ERROR("f_start should be in Angstrom","sxcter", 1) # exclude abs frequencies and spatial frequencies
-		else: freq_start = old_div(1.,options.f_start)
+		else: freq_start = 1./options.f_start
 
 	if options.f_stop >0.0:
 		if options.f_stop  <=0.5: ERROR("f_stop should be in Angstrom","sxcter", 1) # exclude abs frequencies and spatial frequencies
-		else: freq_stop = old_div(1.,options.f_stop)
+		else: freq_stop = 1./options.f_stop
 
 	while True:
 		# --------------------------------------------------------------------------------