def makevol(options,
originalseriesfile,
newseries,
it,
originalangles,
originalsize,
writevols=1,
initialfsc=0):
#print "Newseries received in makevol and its type are", type(newseries)
#print newseries
#sys.exit()
mode = 'gauss_2'
if options.reconstructor:
if len(options.reconstructor) > 1:
if 'mode' in options.reconstructor[-1]:
try:
if options.reconstructor[-1]['mode'] != 'gauss_2':
mode = options.reconstructor[-1]['mode']
else:
pass
except:
pass
box = originalsize
if options.pad3d:
if options.pad2d:
if options.pad3d > options.pad2d:
box = int(box * options.pad3d)
else:
box = int(box * options.pad2d)
else:
box = int(box * options.pad3d)
elif options.pad2d:
box = int(box * options.pad2d)
#if options.verbose > 5:
#print "\nPPPPPPPPPPPPPPP\n\n(e2spt_isr.py)(makevol) Because there's options.pad=%f,then newsize=%d" % ( options.pad3d, newsize )
#if options.verbose > 9:
#print "\n(e2spt_isr.py)(makevol) Mode for reconstructor is", mode
#print "Setting up reconstructor; options.reconstructor is", options.reconstructor
#print "For volume of size",box,box,box
#rEven = Reconstructors.get(options.reconstructor[0],{'size':(box,box,box),'sym':'c1','verbose':True,'mode':mode})
r = Reconstructors.get(options.reconstructor[0], {
'size': (box, box, box),
'sym': 'c1',
'verbose': False,
'mode': mode
})
r.setup()
#print "in isr reconstructor is", options.reconstructor
#print "r is", r
#print "and box was", box
axis = 'y'
if options.tiltaxis:
axis = options.tiltaxis
angles = []
#print "\n++++++++++++++++++++++++++++++\n(makevol) file=%s, lowmostRAWangle=%f, upmostRAWangle=%f" % ( originalseriesfile, min(originalangles), max(originalangles) )
#print "However, adding projections, the total number of images and angles will be", len(newseries),len(originalangles)
#print "\n++++++++++++++++++++++++++++++\n"
apix = 1.0
imageslist = []
for tiltangle in originalangles:
#print "Angle and type are", tiltangle, type(tiltangle)
img = newseries[tiltangle]
#try:
# if img['spt_tiltangle']:
# pass
#except:
img['xform.projection'] = Transform({
'type': 'eman',
'az': 90,
'alt': float(tiltangle),
'phi': -90
})
img2send = img.copy()
imageslist.append(img2send)
#print "size of image appended to imageslist", img2send['nx'],img2send['ny']
apix = img['apix_x']
angle = None
if options.verbose > 9:
print(
"\n(e2spt_isr.py)(makevol) processing image %d in stack %s and ITERATION %d"
% (i, originalseriesfile, it))
print(
"For image %d, mean=%f, min=%f, max=%f, std=%f" %
(i, img['mean'], img['minimum'], img['maximum'], img['sigma']))
if options.pad2d and float(options.pad2d) > 1.0:
box2d = img['nx'] * options.pad2d
img = clip2D(img, box2d)
#print "\nPadding prj to newsize", newsize
try:
angle = img['spt_tiltangle']
except:
print(
"\nWARNING: 'spt_tiltangle' parameter not found in the header of image %d in file %s"
% (i, f))
#sys.exit()
angle = tiltangle
print("Using this tiltangle", tiltangle)
try:
axis = img['spt_tiltaxis']
except:
if options.verbose > 9:
print(
"""\n(e2spt_isr.py)(makevol) WARNING:
No spt_tiltaxis or sptsim_tiltaxis found in header. Default used.""",
options.tiltaxis, axis)
if angle != None:
#angles.append( angle )
t = Transform({'type': 'eman', 'az': 90, 'alt': angle, 'phi': -90})
if axis == 'x':
t = Transform({'type': 'eman', 'alt': angle})
imgp = r.preprocess_slice(img, t)
weight = 1.0
if options.verbose > 9:
print("\n(makevol) ITER=%d, tiltangle=%f, weight=%f" %
(it, angle, weight))
print("Inserted IMAGE with this tranform", t)
#print "transform used for WHOLE 3D", t
r.insert_slice(imgp, t, weight)
rec = r.finish(True)
rec['apix_x'] = apix
rec['apix_y'] = apix
rec['apix_z'] = apix
rec['origin_x'] = 0
rec['origin_y'] = 0
rec['origin_z'] = 0
#angles.sort()
#if options.verbose > 9:
# print "\n(e2spt_fillwedge.py)(makevol) Sorted angles to write to header are", angles
rec['spt_tiltangles'] = originalangles
recxc = old_div(rec['nx'], 2)
recyc = old_div(rec['ny'], 2)
reczc = old_div(rec['nz'], 2)
#R2 = Region( (2*recxc - originalsize)/2, (2*recyc - originalsize)/2, (2*reczc - originalsize)/2, originalsize , originalsize , originalsize)
#rec.clip_inplace( R2 )
outx = outy = outz = originalsize
if options.outxsize:
outx = options.outxsize
if options.outysize:
outy = options.outysize
if options.outzsize:
outz = options.outzsize
rec = clip3D(rec, outx, outy, outz)
rec.process_inplace('normalize')
if options.verbose > 9:
print("\n(e2spt_isr.py)(makevol) Reconstructed volume for file",
originalseriesfile)
volfile = ''
if options.savevols and writevols:
volfile = os.path.basename(originalseriesfile).replace(
'.hdf', '_ISR3D.hdf')
if options.path not in volfile:
volfile = options.path + '/' + volfile
rec.write_image(volfile, 0)
#print "size of images in imageslist to send is", imageslist[0]['nx'],imageslist[-1]['ny']
ret = genOddAndEvenVols(options, originalseriesfile, imageslist)
volOdd = ret[1]
volEven = ret[0]
score3d = ret[2]
#volOdd.write_image( options.path + '/' + originalseriesfile.replace('.hdf','_ISR3D_ODD.hdf') )
#volEven.write_image( options.path + '/' + originalseriesfile.replace('.hdf','_ISR3D_EVEN.hdf') )
filebasetoplotfsc = originalseriesfile
if it == 0:
print("There SHOULD be intialfsc", initialfsc)
if initialfsc:
print("There is intialfsc", initialfsc)
filebasetoplotfsc = originalseriesfile.replace('.hdf', '_INITIAL.hdf')
retfsc = fscOddVsEven(options, filebasetoplotfsc, volOdd, volEven)
fsc = retfsc[0]
fscarea = retfsc[1]
aliscore = []
return [rec, volfile, fscarea, score3d]
def makevol(options, originalseriesfile, newseries, it, originalangles, originalsize, writevols=1, initialfsc=0):
# print "Newseries received in makevol and its type are", type(newseries)
# print newseries
# sys.exit()
mode = "gauss_2"
if options.reconstructor:
if len(options.reconstructor) > 1:
if "mode" in options.reconstructor[-1]:
try:
if options.reconstructor[-1]["mode"] != "gauss_2":
mode = options.reconstructor[-1]["mode"]
else:
pass
except:
pass
box = originalsize
if options.pad3d:
if options.pad2d:
if options.pad3d > options.pad2d:
box = int(box * options.pad3d)
else:
box = int(box * options.pad2d)
else:
box = int(box * options.pad3d)
elif options.pad2d:
box = int(box * options.pad2d)
# if options.verbose > 5:
# print "\nPPPPPPPPPPPPPPP\n\n(e2spt_isr.py)(makevol) Because there's options.pad=%f,then newsize=%d" % ( options.pad3d, newsize )
# if options.verbose > 9:
# print "\n(e2spt_isr.py)(makevol) Mode for reconstructor is", mode
# print "Setting up reconstructor; options.reconstructor is", options.reconstructor
# print "For volume of size",box,box,box
# rEven = Reconstructors.get(options.reconstructor[0],{'size':(box,box,box),'sym':'c1','verbose':True,'mode':mode})
r = Reconstructors.get(
options.reconstructor[0], {"size": (box, box, box), "sym": "c1", "verbose": False, "mode": mode}
)
r.setup()
# print "in isr reconstructor is", options.reconstructor
# print "r is", r
# print "and box was", box
axis = "y"
if options.tiltaxis:
axis = options.tiltaxis
angles = []
# print "\n++++++++++++++++++++++++++++++\n(makevol) file=%s, lowmostRAWangle=%f, upmostRAWangle=%f" % ( originalseriesfile, min(originalangles), max(originalangles) )
# print "However, adding projections, the total number of images and angles will be", len(newseries),len(originalangles)
# print "\n++++++++++++++++++++++++++++++\n"
apix = 1.0
imageslist = []
for tiltangle in originalangles:
# print "Angle and type are", tiltangle, type(tiltangle)
img = newseries[tiltangle]
# try:
# if img['spt_tiltangle']:
# pass
# except:
img["xform.projection"] = Transform({"type": "eman", "az": 90, "alt": float(tiltangle), "phi": -90})
img2send = img.copy()
imageslist.append(img2send)
# print "size of image appended to imageslist", img2send['nx'],img2send['ny']
apix = img["apix_x"]
angle = None
if options.verbose > 9:
print "\n(e2spt_isr.py)(makevol) processing image %d in stack %s and ITERATION %d" % (
i,
originalseriesfile,
it,
)
print "For image %d, mean=%f, min=%f, max=%f, std=%f" % (
i,
img["mean"],
img["minimum"],
img["maximum"],
img["sigma"],
)
if options.pad2d and float(options.pad2d) > 1.0:
box2d = img["nx"] * options.pad2d
img = clip2D(img, box2d)
# print "\nPadding prj to newsize", newsize
try:
angle = img["spt_tiltangle"]
except:
print "\nWARNING: 'spt_tiltangle' parameter not found in the header of image %d in file %s" % (i, f)
# sys.exit()
angle = tiltangle
print "Using this tiltangle", tiltangle
try:
axis = img["spt_tiltaxis"]
except:
if options.verbose > 9:
print """\n(e2spt_isr.py)(makevol) WARNING:
No spt_tiltaxis or sptsim_tiltaxis found in header. Default used.""", options.tiltaxis, axis
if angle != None:
# angles.append( angle )
t = Transform({"type": "eman", "az": 90, "alt": angle, "phi": -90})
if axis == "x":
t = Transform({"type": "eman", "alt": angle})
imgp = r.preprocess_slice(img, t)
weight = 1.0
if options.verbose > 9:
print "\n(makevol) ITER=%d, tiltangle=%f, weight=%f" % (it, angle, weight)
print "Inserted IMAGE with this tranform", t
# print "transform used for WHOLE 3D", t
r.insert_slice(imgp, t, weight)
rec = r.finish(True)
rec["apix_x"] = apix
rec["apix_y"] = apix
rec["apix_z"] = apix
rec["origin_x"] = 0
rec["origin_y"] = 0
rec["origin_z"] = 0
# angles.sort()
# if options.verbose > 9:
# print "\n(e2spt_fillwedge.py)(makevol) Sorted angles to write to header are", angles
rec["spt_tiltangles"] = originalangles
recxc = rec["nx"] / 2
recyc = rec["ny"] / 2
reczc = rec["nz"] / 2
# R2 = Region( (2*recxc - originalsize)/2, (2*recyc - originalsize)/2, (2*reczc - originalsize)/2, originalsize , originalsize , originalsize)
# rec.clip_inplace( R2 )
outx = outy = outz = originalsize
if options.outxsize:
outx = options.outxsize
if options.outysize:
outy = options.outysize
if options.outzsize:
outz = options.outzsize
rec = clip3D(rec, outx, outy, outz)
rec.process_inplace("normalize")
if options.verbose > 9:
print "\n(e2spt_isr.py)(makevol) Reconstructed volume for file", originalseriesfile
volfile = ""
if options.savevols and writevols:
volfile = os.path.basename(originalseriesfile).replace(".hdf", "_ISR3D.hdf")
if options.path not in volfile:
volfile = options.path + "/" + volfile
rec.write_image(volfile, 0)
# print "size of images in imageslist to send is", imageslist[0]['nx'],imageslist[-1]['ny']
ret = genOddAndEvenVols(options, originalseriesfile, imageslist)
volOdd = ret[1]
volEven = ret[0]
score3d = ret[2]
# volOdd.write_image( options.path + '/' + originalseriesfile.replace('.hdf','_ISR3D_ODD.hdf') )
# volEven.write_image( options.path + '/' + originalseriesfile.replace('.hdf','_ISR3D_EVEN.hdf') )
filebasetoplotfsc = originalseriesfile
if it == 0:
print "There SHOULD be intialfsc", initialfsc
if initialfsc:
print "There is intialfsc", initialfsc
filebasetoplotfsc = originalseriesfile.replace(".hdf", "_INITIAL.hdf")
retfsc = fscOddVsEven(options, filebasetoplotfsc, volOdd, volEven)
fsc = retfsc[0]
fscarea = retfsc[1]
aliscore = []
return [rec, volfile, fscarea, score3d]