Python EMApp.exec_方法代码示例

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	
	usage="[prog] <2D image file> "
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	(options, args) = parser.parse_args()
	logid=E2init(sys.argv)


	
	filename=args[0]
	
	app = EMApp()
	img=EMData(filename)
	
	
	#print img[0]["mean"]
	w=EMBreakBrick(img,app)
	#w.set_data(img,filename)
	
	app.show_specific(w)
	app.exec_()
	
	
	
	
	
	E2end(logid)

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog 3Dstack [options]
	Visulaizse and compute the mean amplitude and sigma in the missing wedge region. After you are sasified that the missing wedge looks sane, compute missing wedge stats
	on all volumes. These stats are used by the aligner tomo.fsc, for subtomogram alignment and averaging.
	"""
	
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	
	parser.add_pos_argument(name="tdstack",help="The 3D stack to examine.", default="", guitype='filebox',  row=0, col=0,rowspan=1, colspan=2)
	parser.add_header(name="wedgeheader", help='Options below this label are specific to e2wedge', title="### e2wedge options ###", row=1, col=0, rowspan=1, colspan=2)
	parser.add_argument("--wedgeangle",type=float,help="Missing wedge angle",default=60.0, guitype='floatbox', row=2, col=0, rowspan=1, colspan=1)
	parser.add_argument("--wedgei",type=float,help="Missingwedge begining", default=0.05)
	parser.add_argument("--wedgef",type=float,help="Missingwedge ending", default=0.5)
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
	parser.add_argument("--nogui", action="store_true", default=False, help="Do not launch the GUI and set the average of the missing wedge statistics on all the volumes.")
	parser.add_argument("--averagestats", action="store_true", default=False, help="Do not launch the GUI and set the average of the missing wedge statistics on all the volumes.")

	(options, args) = parser.parse_args()
	
	stack=args[0]
	
	if not options.nogui:	
		em_app = EMApp()
		wedgeviewer = MissingWedgeViewer(stack, options.wedgeangle, wedgei=options.wedgei, wedgef=options.wedgef)
		wedgeviewer.show()
		ret=em_app.exec_()
		sys.exit(ret)
	else:
		means=[]
		sigmas=[]
		
		n=EMUtil.get_image_count(stack)
		for i in range(n):
			a = EMData(stack,i)
			retr = wedgestats(a,options.wedgeangle,options.wedgei,options.wedgef)
			mean = retr[0]
			sigma = retr[1]
			
			if options.averagestats:
				means.append(mean)
				sigmas.append(sigma)
			else:
				a['spt_wedge_mean'] = mean
				a['spt_wedge_sigma'] = sigma
				print "The mean and sigma for subvolume %d are: mean=%f, sigma=%f" % (i,mean,sigma)
				a.write_image(stack,i)
		
		if options.averagestats:
			meanavg = sum(means)/len(means)
			sigmaavg = sum(sigmas)/len(sigmas)
			
			print "The average mean and sigma for the wedges in the stack are", meanavg, sigmaavg
			for i in range(n):
				a = EMData(stack,i)
				a['spt_wedge_mean'] = meanavg
				a['spt_wedge_sigma'] = sigmaavg
				a.write_image(stack,i)
	return()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def display_validation_plots(path, radcut, planethres, plotdatalabels=False, color='#00ff00', plotzaxiscolor=False):
	from emimage2d import EMImage2DWidget
	from emapplication import EMApp
	r = []
	theta = []
	datap = []
	zaxis = []
	
	try:
		tpdb = js_open_dict("%s/perparticletilts.json"%path)
		tplist = tpdb["particletilt_list"]
		maxcolorval = max(tplist, key=lambda x: x[3])[3]

		for tp in tplist:
			if tp[3] > planethres:	# if the out of plane threshold is too much
				continue
			if plotdatalabels: datap.append(tp[0])
			r.append(tp[1])
			theta.append(math.radians(tp[2]))
			# Color the Z axis out of planeness
			zaxis.append(computeRGBcolor(tp[3],0,maxcolorval))
		tpdb.close()
	except:
		print "Couldn't load tp from DB, not showing polar plot"
	data = None	
	try:
		data = EMData("%s/contour.hdf"%path)
	except:
		print "Couldn't open contour plot"
	
	if not data and not (theta and r): return
	app = EMApp()
	if theta and r:
		plot = EMValidationPlot()
		plot.set_data((theta,r),50,radcut,datap)
		# Color by Z axis if desired
		if plotzaxiscolor: plot.set_scattercolor([zaxis])
		plot.set_datalabelscolor(color)
		plot.show()
	if data:
		image = EMImage2DWidget(data)
		image.show()
	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = progname + """ [options] <xml>
	Convert xml to txt and optionally display them.
	"""
	
	args_def = {'display':1}	
	parser = argparse.ArgumentParser()
	parser.add_argument("xml", nargs='*', help="specify xml files to be processed")
	parser.add_argument("-d", "--display", type=int, help="disply (1) or not (0), by default {}".format(args_def['display']))
	args = parser.parse_args()
	
	if len(sys.argv) == 1:
		print "usage: " + usage
		print "Please run '" + progname + " -h' for detailed options."
		sys.exit(1)
	# get default values
	for i in args_def:
		if args.__dict__[i] == None:
			args.__dict__[i] = args_def[i]
	#		
	for xml in args.xml:
		with open(xml+'.txt', 'w') as w_txt:
			for coord in XE.parse(xml).getroot():
				for xy in coord:
					if xy.tag == 'x':
						w_txt.write(xy.text + '\t')
					else:
						w_txt.write(xy.text + '\n')
	# display
	if args.display == 1:
		app = EMApp()
		for xml in args.xml:
			filename = xml+'.txt'
			w = EMWidgetFromFile(filename,application=app,force_2d=False)
			w.setWindowTitle(base_name(filename))
			app.show_specific(w)
		app.exec_()			

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])

	usage = """prog [options]
A simple CTF simulation program. Doesn't read or process data. Just does mathematical simulations.
"""

	parser = EMArgumentParser(usage=usage,version=EMANVERSION)

	parser.add_argument("--apix",type=float,help="Angstroms per pixel for all images",default=1.0, guitype='floatbox', row=4, col=0, rowspan=1, colspan=1, mode="autofit['self.pm().getAPIX()']")
	parser.add_argument("--voltage",type=float,help="Microscope voltage in KV",default=300.0, guitype='floatbox', row=4, col=1, rowspan=1, colspan=1, mode="autofit['self.pm().getVoltage()']")
	parser.add_argument("--cs",type=float,help="Microscope Cs (spherical aberation)",default=4.1, guitype='floatbox', row=5, col=0, rowspan=1, colspan=1, mode="autofit['self.pm().getCS()']")
	parser.add_argument("--ac",type=float,help="Amplitude contrast (percentage, default=10)",default=10, guitype='floatbox', row=5, col=1, rowspan=1, colspan=1, mode='autofit')
	parser.add_argument("--samples",type=int,help="Number of samples in the plotted curve",default=256)
	parser.add_argument("--verbose", "-v", dest="verbose", action="store", metavar="n", type=int, default=0, help="verbose level [0-9], higner number means higher level of verboseness")

	(options, args) = parser.parse_args()

	from emapplication import EMApp
	app=EMApp()
	gui=GUIctfsim(app,options.apix,options.voltage,options.cs,options.ac,options.samples)
	gui.show_guis()
	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog [options] 
	This is a program to compute the resolution of a n averaged subtomogram. Right now it is very simple simple divide the aligned
	subtomos into even/odd classes, average and then compute the FSC. In the future this program will be extended to compute 
	resolution of an averged subtomo vs a reference and hopefuly of a single sub/tomogram.
	"""
	
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	
	parser.add_pos_argument(name="tomodir",help="The refinement directory to use for tomoresolution.", default="", guitype='dirbox', dirbasename='spt_',  row=0, col=0,rowspan=1, colspan=2)
	parser.add_header(name="tomoresoheader", help='Options below this label are specific to e2tomoresolution', title="### e2tomoresolution options ###", row=1, col=0, rowspan=1, colspan=2)
	parser.add_argument("--averager",type=str,help="The averager used to generate the averages. Default is \'mean\'.",default="mean", guitype='combobox', choicelist='dump_averagers_list()', row=2, col=0, rowspan=1, colspan=2)
	parser.add_argument("--sym",  type=str,help="The recon symmetry", default="c1", guitype='symbox', row=3, col=0, rowspan=1, colspan=2)
	parser.add_argument("--mask", type=str,help="The mask to apply before FSC calculation", default=None, guitype='comboparambox', choicelist='re_filter_list(dump_processors_list(),\'mask\')', row=4, col=0, rowspan=1, colspan=2)
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
	
	(options, args) = parser.parse_args()
	if options.mask: options.mask = parsemodopt(options.mask)
	
	logid=E2init(sys.argv,options.ppid)
	
	fscstrategy = EvenOddReso(args[0], options)
	fscstrategy.execute()
	
	results_db = db_open_dict("bdb:%s#convergence.results"%args[0])
	results_db["tomo_fsc"] = [fscstrategy.getFreq(),fscstrategy.getFSC(),fscstrategy.getError()]
	results_db.close()
	
	E2end(logid)
	
	# Plot FSC
	app = EMApp()
	plot = EMPlot2DWidget()
	plot.set_data((fscstrategy.getFreq(),fscstrategy.getFSC()))
	plot.show()
	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	global debug,logid
	progname = os.path.basename(sys.argv[0])
	usage = """%prog [options]

This program allows the user to play around with Fourier synthesis graphically
	
"""

	parser = OptionParser(usage=usage,version=EMANVERSION)

#	parser.add_option("--gui",action="store_true",help="Start the GUI for interactive fitting",default=False)
	parser.add_option("--verbose", "-v", dest="verbose", action="store", metavar="n", type="int", default=0, help="verbose level [0-9], higner number means higher level of verboseness")
	
	(options, args) = parser.parse_args()

	app=EMApp()
	win=GUIFourierSynth(app)
	win.show()
	try: 
		win.raise_()
		win.synthplot.raise_()
	except: pass
	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]

#.........这里部分代码省略.........
	parser.add_option("--voltage",type="float",help="Microscope voltage in KV",default=0)
	parser.add_option("--cs",type="float",help="Microscope Cs (spherical aberation)",default=0)
	parser.add_option("--ac",type="float",help="Amplitude contrast (percentage, default=10)",default=10)
	parser.add_option("--autohp",action="store_true",help="Automatic high pass filter of the SNR only to remove initial sharp peak, phase-flipped data is not directly affected (default false)",default=False)
	#parser.add_option("--invert",action="store_true",help="Invert the contrast of the particles in output files (default false)",default=False)
	parser.add_option("--nonorm",action="store_true",help="Suppress per image real-space normalization",default=False)
	parser.add_option("--nosmooth",action="store_true",help="Disable smoothing of the background (running-average of the log with adjustment at the zeroes of the CTF)",default=False)
	#parser.add_option("--phaseflip",action="store_true",help="Perform phase flipping after CTF determination and writes to specified file.",default=False)
	#parser.add_option("--wiener",action="store_true",help="Wiener filter (optionally phaseflipped) particles.",default=False)
	parser.add_option("--oversamp",type="int",help="Oversampling factor",default=1)
	parser.add_option("--sf",type="string",help="The name of a file containing a structure factor curve. Can improve B-factor determination.",default=None)
	parser.add_option("--debug",action="store_true",default=False)
	
	(options, args) = parser.parse_args()

	if len(args)<1 : parser.error("Input image required")
	
	if global_def.CACHE_DISABLE:
		from utilities import disable_bdb_cache
		disable_bdb_cache()

	if options.auto_fit:
		if options.voltage==0 : parser.error("Please specify voltage")
		if options.cs==0 : parser.error("Please specify Cs")
	if options.apix==0 : print "Using A/pix from header"
		
	debug=options.debug

	global sfcurve
	if options.sf :
		sfcurve=XYData()
		sfcurve.read_file(options.sf)

	logid=E2init(sys.argv)

#	if options.oversamp>1 : options.apix/=float(options.oversamp)

	db_project=db_open_dict("bdb:project")
	db_parms=db_open_dict("bdb:e2ctf.parms")
	db_misc=db_open_dict("bdb:e2ctf.misc")

	options.filenames = args
	### Power spectrum and CTF fitting
	if options.auto_fit:
		img_sets=pspec_and_ctf_fit(options,debug) # converted to a function so to work with the workflow
		
		### This computes the intensity of the background subtracted power spectrum at each CTF maximum for all sets
		global envelopes # needs to be a global for the Simplex minimizer
		# envelopes is essentially a cache of information that could be useful at later stages of refinement
		# as according to Steven Ludtke
		for i in img_sets:
			envelopes.append(ctf_env_points(i[2],i[3],i[1]))

		# we use a simplex minimizer to try to rescale the individual sets to match as best they can
		scales=[1.0]*len(img_sets)
		if (len(img_sets)>3) :
			incr=[0.2]*len(img_sets)
			simp=Simplex(env_cmp,scales,incr)
			scales=simp.minimize(maxiters=1000)[0]
	#		print scales
			print " "

		# apply the final rescaling
		envelope=[]
		for i in range(len(scales)):
			cur=envelopes[i]
			for j in range(len(cur)):
				envelope.append((cur[j][0],cur[j][1]*scales[i]))

		envelope.sort()
		envelope=[i for i in envelope if i[1]>0]	# filter out all negative peak values

		db_misc=db_open_dict("bdb:e2ctf.misc")
		db_misc["envelope"]=envelope
		#db_close_dict("bdb:e2ctf.misc")

		#out=file("envelope.txt","w")
		#for i in envelope: out.write("%f\t%f\n"%(i[0],i[1]))
		#out.close()

	### GUI - user can update CTF parameters interactively
	if options.gui :
		img_sets = get_gui_arg_img_sets(options.filenames)
		if len(img_sets) == 0:
			E2end(logid)
			sys.exit(1)
		app=EMApp()
		gui=GUIctf(app,img_sets)
		gui.show_guis()
		app.exec_()

		print "done execution"

	### Process input files
	#if debug : print "Phase flipping / Wiener filtration"
	# write wiener filtered and/or phase flipped particle data to the local database
	#if options.phaseflip or options.wiener: # only put this if statement here to make the program flow obvious
	#	write_e2ctf_output(options) # converted to a function so to work with the workflow

	E2end(logid)

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog [options] <image file> ...

	This program can be used to visualize most files used in EMAN2. Running it without arguments
	will open a browser window with more flexible functionality than the command-line.
	
	"""
	global app,win,options

	parser = EMArgumentParser(usage=usage,version=EMANVERSION)

	parser.add_argument("--classmx",type=str,help="<classmx>,<#> Show particles in one class from a classification matrix. Pass raw particle file as first argument to command.")
	parser.add_argument("--classes",type=str,help="<rawptcl>,<classmx> Show particles associated class-averages")
	parser.add_argument("--pdb",type=str,help="<pdb file> Show PDB structure.")
	parser.add_argument("--singleimage",action="store_true",default=False,help="Display a stack in a single image view")
	parser.add_argument("--plot",action="store_true",default=False,help="Data file(s) should be plotted rather than displayed in 2-D")
	parser.add_argument("--plot3",action="store_true",default=False,help="Data file(s) should be plotted rather than displayed in 3-D")
	parser.add_argument("--fullrange",action="store_true",default=False,help="A specialized flag that disables auto contrast for the display of particles stacks and 2D images only.")
	parser.add_argument("--newwidget",action="store_true",default=False,help="Use the new 3D widgetD. Highly recommended!!!!")
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-2)
	parser.add_argument("--verbose", "-v", dest="verbose", action="store", metavar="n", type=int, default=0, help="verbose level [0-9], higner number means higher level of verboseness")

	(options, args) = parser.parse_args()

#	logid=E2init(sys.argv)

	app = EMApp()
	#gapp = app
	#QtGui.QApplication(sys.argv)
	win=[]
	if options.fullrange:
		fullrangeparms = set_full_range()
	
	if len(args) < 1:
		global dialog
		file_list = []
		dialog = embrowser.EMBrowserWidget(withmodal=False,multiselect=False)
		dialog.show()
		try: dialog.raise_()
# 			QtCore.QObject.connect(dialog,QtCore.SIGNAL("ok"),on_browser_done)
# 			QtCore.QObject.connect(dialog,QtCore.SIGNAL("cancel"),on_browser_cancel)
		except: pass
	
	elif options.pdb:
		load_pdb(args,app)
	
	elif options.plot:
		plot(args,app)
		
	elif options.plot3:
		plot_3d(args,app)
		
	elif options.classes:
		options.classes=options.classes.split(",")
		imgs=EMData.read_images(args[0])
		display(imgs,app,args[0])

		QtCore.QObject.connect(win[0].child,QtCore.SIGNAL("mousedown"),lambda a,b:selectclass(options.classes[0],options.classes[1],a,b))
		try:
			out=file("selected.lst","w")
			out.write("#LST\n")
			out.close()
		except: pass
		
	elif options.classmx:
		options.classmx=options.classmx.split(",")
		clsnum=int(options.classmx[1])
		imgs=getmxim(args[0],options.classmx[0],clsnum)
		display(imgs,app,args[0])
	
	else:
		for i in args:
			if not file_exists(i):
				print "%s doesn't exist" %i
				sys.exit(1)
			display_file(i,app,options.singleimage,usescenegraph=options.newwidget)
	
	if options.fullrange:
		revert_full_range(fullrangeparms)

	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog [options] <image> <image2>....

	The even newer version of e2boxer. Complete rewrite. Incomplete.
	
	This program 
"""
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)

	parser.add_pos_argument(name="micrographs",help="List the file to process with e2boxer here.", default="", guitype='filebox', browser="EMBoxesTable(withmodal=True,multiselect=True)",  row=0, col=0,rowspan=1, colspan=3, mode="boxing,extraction")
	parser.add_argument("--invert",action="store_true",help="If specified, inverts input contrast. Particles MUST be white on a darker background.",default=False, guitype='boolbox', row=3, col=2, rowspan=1, colspan=1, mode="extraction")
	parser.add_argument("--boxsize","-B",type=int,help="Box size in pixels",default=-1, guitype='intbox', row=2, col=0, rowspan=1, colspan=3, mode="boxing,extraction")
	parser.add_argument("--ptclsize","-P",type=int,help="Longest axis of particle in pixels (diameter, not radius)",default=-1, guitype='intbox', row=2, col=0, rowspan=1, colspan=3, mode="boxing,extraction")
	parser.add_argument("--apix",type=float,help="Angstroms per pixel for all images",default=-1, guitype='floatbox', row=4, col=0, rowspan=1, colspan=1, mode="autofit['self.pm().getAPIX()']")
	parser.add_argument("--voltage",type=float,help="Microscope voltage in KV",default=-1, guitype='floatbox', row=4, col=1, rowspan=1, colspan=1, mode="autofit['self.pm().getVoltage()']")
	parser.add_argument("--cs",type=float,help="Microscope Cs (spherical aberation)",default=-1, guitype='floatbox', row=5, col=0, rowspan=1, colspan=1, mode="autofit['self.pm().getCS()']")
	parser.add_argument("--ac",type=float,help="Amplitude contrast (percentage, default=10)",default=10, guitype='floatbox', row=5, col=1, rowspan=1, colspan=1, mode='autofit')
	parser.add_argument("--no_ctf",action="store_true",default=False,help="Disable CTF determination", guitype='boolbox', row=3, col=0, rowspan=1, colspan=1, mode="extraction")
	parser.add_argument("--autopick",type=str,default=None,help="Perform automatic particle picking. Provide mode and parameter string")
	parser.add_argument("--write_dbbox",action="store_true",default=False,help="Export EMAN1 .box files",guitype='boolbox', row=3, col=0, rowspan=1, colspan=1, mode="extraction")
	parser.add_argument("--write_ptcls",action="store_true",default=False,help="Extract selected particles from micrographs and write to disk", guitype='boolbox', row=3, col=1, rowspan=1, colspan=1, mode="extraction[True]")
	parser.add_argument("--gui", action="store_true", default=False, help="Interactive GUI mode")
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
	parser.add_argument("--verbose", "-v", dest="verbose", action="store", metavar="n", type=int, default=0, help="verbose level [0-9], higner number means higher level of verboseness")

	(options, args) = parser.parse_args()
	
	global invert_on_read
	if options.invert : invert_on_read = True


	#####
	# Parameter Validation
	project_db = js_open_dict("info/project.json")

	if not (options.gui or options.write_ptcls or options.write_dbbox or options.autopick):
		print "Error: No actions specified. Try --gui for interactive/semi-automated particle picking." 

	if not options.no_ctf :
		if options.voltage>1500 :
			options.voltage/=1000
			print "Voltage specified in kV. Adjusting specified value to ",options.voltage
		if options.voltage<10 :
			try: 
				options.voltage=project_db["global.microscope_voltage"]
				print "Using project voltage of ",options.voltage,"kV"
			except:
				print "Error: No voltage specified, and no project settings available. Disabling CTF mode."
				options.no_ctf=True
		if options.cs<0 :
			try:
				options.cs=project_db["global.microscope_cs"]
				print "Using project Cs of ",options.cs,"mm"
			except:
				print "Error: No Cs specified, and no project settings available. Disabling CTF mode."
				options.no_ctf=True
		if options.ac<0 and not options.no_ctf:
			print "Error: Invalid %AC value. Disabling CTF mode."
			options.no_ctf=True
		if options.ac<1.0 :
			print "Warning: %AC should be specified as a %. If you intended a %AC>1%, please try again. Will proceed with the specified value"
	
	if options.apix<=0 :
		try:
			options.apix=project_db["global.apix"]
			print "Warning: No A/pix specified. Using ",options.apix," from project. Please insure this is correct for the images being boxed!"
		except:
			print "Error: Value required for A/pixel. If this is a non TEM image, suggest --apix=1 and --no_ctf."
			sys.exit(1)
		
	logid=E2init(sys.argv,options.ppid)

	if options.autopick!=None :
		pass

	if options.gui :
		if isinstance(QtGui,nothing) :
			print "====================================="
			print "ERROR: GUI mode unavailable without PyQt4"
			sys.exit(1)
		from emapplication import EMApp
		app=EMApp()
		gui=GUIBoxer(args,options.voltage,options.apix,options.cs,options.ac,options.boxsize,options.ptclsize)
		gui.show()
		app.exec_()

	if options.write_dbbox:
		pass
	
	if options.write_ptcls:
		pass
		

	E2end(logid)

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	helpstring =  """Help is available on the following topics:
processors, cmps, aligners, averagers, projectors, reconstructors, analyzers, symmetries, orientgens, rotationtypes"""
	usage = """prog <topic> [contains]
	
Interactive help on a variety of the eman2 library's modular functions. The optional 'contains' argument will
act as a filter on the names of the algorithms."""
	usage += " "+helpstring

	parser = EMArgumentParser(usage=usage,version=EMANVERSION)

	#parser.add_argument("--res", "-R", type=float, help="Resolution in A, equivalent to Gaussian lowpass with 1/e width at 1/res",default=2.8)
	#parser.add_argument("--box", "-B", type=str, help="Box size in pixels, <xyz> or <x>,<y>,<z>")
	parser.add_argument("--gui", action="store_true", help="Use the GUI for display help", default=False)
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-2)
	parser.add_argument("--verbose", "-v", dest="verbose", action="store", metavar="n", type=int, default=0, help="verbose level [0-9], higner number means higher level of verboseness")
	
	(options, args) = parser.parse_args()
		
	if options.gui:
		from e2projectmanager import TheHelp
		from emapplication import EMApp
		app = EMApp()
		thehelp = TheHelp()
		thehelp.show()
		if args:
			print args[0]
			if args[0] in ("aligner","aligners"):
				thehelp._helpchange(0)
			elif args[0] in ("analyzer","analyzers"):
				thehelp._helpchange(1)
			elif args[0] in ("averager","averagers"):
				thehelp._helpchange(2)
			elif args[0] in ("cmp","cmps"):
				thehelp._helpchange(3)
			elif args[0] in ("orientgen","orientationgen","orientgens","orientationgens","orientationgenerators"):
				thehelp._helpchange(4)
			elif args[0] in ("processor","processors"):
				thehelp._helpchange(5)
			elif args[0] in ("projector","projectors"):
				thehelp._helpchange(6)
			elif args[0] in ("reconstructor","reconstructors"):
				thehelp._helpchange(7)
			elif args[0] in ("sym","symmetry","symmetries"):
				thehelp._helpchange(8)
		app.exec_()
		exit(0)

	if len(args)<1 : 
		print helpstring
		exit(0)
		
	l=None
	if args[0] in ("cmp","cmps") :
		print "Available comparators:"
		l=dump_cmps_list()
	elif args[0] in ("analyzer","analyzers") :
		print "Available analysers:"
		l=dump_analyzers_list()
	elif args[0] in ("averager","averagers") :
		print "Available averagers:"
		l=dump_averagers_list()
	elif args[0] in ("processor","processors") :
		print "Available processors:"
		l=dump_processors_list()
	elif args[0] in ("projector","projectors") :
		print "Available projectors:"
		l=dump_projectors_list()
	elif args[0] in ("reconstructor","reconstructors") :
		print "Available reconstructors:"
		l=dump_reconstructors_list()
	elif args[0] in ("aligner","aligners") :
		print "Available aligners:"
		l=dump_aligners_list()
	elif args[0] in ("sym","symmetry","symmetries") :
		print "Available symmetries:"
		l=dump_symmetries_list()
	elif args[0] in ("orientgen","orientationgen","orientgens","orientationgens","orientationgenerators") :
		print "Available orientation generators:"
		l=dump_orientgens_list()
	elif args[0][:8]=="rotation" :
		print "Available rotation conventions:"
		l={"eman":["EMAN convention, az(Z),alt(X),phi(Z') Eulers","alt","FLOAT","Altitude, X-axis","az","FLOAT","Azimuth, Z-axis","phi","FLOAT","Z' Axis. in-plane rotation in 2-D"],
		"imagic":["IMAGIC convention","alpha","FLOAT","alpha","beta","FLOAT","beta","gamma","FLOAT","gamma"],
		"spider":["SPIDER convention","phi","FLOAT","phi","theta","FLOAT","theta","psi","FLOAT","psi"],
		"mrc":["MRC/CCP4 convention","omega","FLOAT","omega","theta","FLOAT","theta","psi","FLOAT","psi"],
		"xyz":["XYZ convention (Chimera)","x","FLOAT","X-axis","y","FLOAT","Y-axis","z","FLOAT","Z-axis"],
		"spin":["Spin-Axis (n1,n2,n3) vector with angle omega","n1","FLOAT","X vector component","n2","FLOAT","Y vector component","n3","FLOAT","Z vector component","omega","FLOAT","Angle of rotation in degrees"],
		"sgirot":["SGI Spin-Axis (n1,n2,n3) vector with angle q","n1","FLOAT","X vector component","n2","FLOAT","Y vector component","n3","FLOAT","Z vector component","q","FLOAT","Angle of rotation in degrees"],
		"quaternion":["Standard 4 component quaternion (e0,e1,e2,e3)","e0","FLOAT","e0","e1","FLOAT","e1","e2","FLOAT","e2","e3","FLOAT","e3"]}

	elif args[0] in ("version"):
	   print EMANVERSION + ' (CVS' + DATESTAMP[6:-2] +')' 
	else:
		print helpstring
		print "unknown option:",args[0]
		
	if l:
		if options.verbose>0:
#.........这里部分代码省略.........

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	
	usage="Generate training set for tomogram segmentation. This program is still experimental. Please consult the developers before using. "
	print usage
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	parser.add_header(name="tmpheader", help='temp label', title="### This program is NOT avaliable yet... ###", row=0, col=0, rowspan=1, colspan=2, mode="box,seg,set")
	#### boxing ####
	parser.add_argument("--boxing",action="store_true",help="Boxing particles.",default=False, guitype='boolbox', row=4, col=0, rowspan=1, colspan=1, mode='box[True]')
	parser.add_pos_argument(name="micrographs",help="List the file to process with e2boxer here.", default="", guitype='filebox', browser="EMRawDataTable(withmodal=True,startpath=\"rawtomograms\")",  row=1, col=0,rowspan=1, colspan=3, mode="box")
	parser.add_argument("--boxsize","-B",type=int,help="Box size in pixels",default=-1, guitype='intbox', row=3, col=0, rowspan=1, colspan=3, mode="box")
	
	#### segment ####
	#parser.add_header(name="instruction", help='instruction', title="### Mark the target features white ###", row=0, col=0, rowspan=1, colspan=2, mode="seg")
	parser.add_argument("--segment",action="store_true",help="Segment particles.",default=False, guitype='boolbox', row=4, col=0, rowspan=1, colspan=1, mode='seg[True]')
	parser.add_pos_argument(name="particles",help="Particle file.", default="", guitype='filebox', browser="EMParticlesTable(withmodal=True)",  row=1, col=0,rowspan=1, colspan=3, mode="seg")
	parser.add_argument("--output", type=str,help="output file name. Default is the input particle file name plus _seg.hdf", default=None,guitype='strbox', row=3, col=0, rowspan=1, colspan=3, mode="seg")
	
	
	#### build set ####
	parser.add_argument("--buildset",action="store_true",help="Segment particles.",default=False, guitype='boolbox', row=7, col=0, rowspan=1, colspan=1, mode='set[True]')
	parser.add_argument("--particles_raw", type=str,help="Input raw particle file", default=None,guitype='filebox',browser="EMParticlesTable(withmodal=True)", row=1, col=0, rowspan=1, colspan=3, mode="set")
	parser.add_argument("--particles_label", type=str,help="Input labels for particle file", default=None,guitype='filebox',browser="EMParticlesTable(withmodal=True)", row=2, col=0, rowspan=1, colspan=3, mode="set")
	parser.add_argument("--boxes_negative", type=str,help="Input boxes of negative samples", default=None,guitype='filebox',browser="EMParticlesTable(withmodal=True)", row=3, col=0, rowspan=1, colspan=3, mode="set")
	parser.add_argument("--ncopy",type=int,help="Number of copies for NEGATIVE samples. (number of copies of particles is calculated accordingly) ",default=20, guitype='intbox', row=5, col=0, rowspan=1, colspan=1, mode="set")
	parser.add_argument("--trainset_output", type=str,help="output file name of the training set.Default is the input particle file name plus _trainset.hdf", default=None,guitype='strbox', row=4, col=0, rowspan=1, colspan=3, mode="set")

	##################
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
	(options, args) = parser.parse_args()
	logid=E2init(sys.argv)
	
	#### boxing ###
	if options.boxing:
		db = js_open_dict(EMBOXERBASE_DB)
		cache_box_size = True
		if options.boxsize == -1:
			cache_box_size = False
			options.boxsize = db.setdefault("box_size",64)

		application = EMApp()
		module = EMBoxerModule(args,options.boxsize)
		module.show_interfaces()

		application.execute(logid)
	
	
	#### segment ###
	if options.segment:
		filename=args[0]
		if options.output==None:
			options.output=filename[:-4]+"_seg.hdf"
		app = EMApp()
		img=EMData.read_images(filename)
		#print img[0]["mean"]
		w=EMImageWidget(data=img,old=None,app=app,force_2d=True)
		#w = EMWidgetFromFile(filename,application=app,force_2d=True)
		w.setWindowTitle(base_name(filename))
		w.show_inspector(1)
		ins=w.get_inspector()
		ins.mmtab.setCurrentIndex(5)
		ins.dtpenv.setText('100')
		w.set_mouse_mode(5)
		app.show_specific(w)
		app.exec_()
		try: os.remove(options.output)
		except:pass
		for e in img:
			e.process_inplace("threshold.belowtozero", {"minval":99})
			e.process_inplace("threshold.binary", {"value":1})
			e.write_image(options.output,-1)
			
	#### build set ###
	
	if options.buildset:
		tomo_in=options.particles_raw
		seg_in=options.particles_label
		neg_in=options.boxes_negative
		if tomo_in and neg_in and seg_in:
			n_ptcl=EMUtil.get_image_count(tomo_in)
			n_neg=EMUtil.get_image_count(neg_in)
			if options.trainset_output==None:
				options.trainset_output=tomo_in[:-4]+"_trainset.hdf"
			p_copy=options.ncopy*n_neg/n_ptcl
		else:
			p_copy=options.ncopy
		try: os.remove(options.trainset_output)
		except: pass
		print "making {} copies for particles, and {} copies for negative samples".format(p_copy,options.ncopy)
		if tomo_in and seg_in:
			n_ptcl=EMUtil.get_image_count(tomo_in)
			for i in range(n_ptcl):
				t=EMData(tomo_in,i)
				s=EMData(seg_in,i)
				for c in range(p_copy):
					tr=Transform()
					rd=random.random()*360
					tr.set_rotation({"type":"2d","alpha":rd})
					e=t.process("xform",{"transform":tr})
					#e.process_inplace("normalize")
					e.write_image(options.trainset_output,-1)
#.........这里部分代码省略.........

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def IPY():
    global ttx
    launch_new_instance()
    # app = TerminalIPythonApp.instance()
    # app.initialize()
    # app.start()

    print "Exiting e22.py"
    ttx = True


def on_timer():
    global ttx

    if ttx:
        QtGui.qApp.quit()


ipythr = threading.Thread(target=IPY)
ipythr.run()


app = EMApp()
EMAN2.GUIMode = True
EMAN2.app = app
mytimer = QtCore.QTimer()
QtCore.QObject.connect(mytimer, QtCore.SIGNAL("timeout()"), on_timer)
mytimer.start(500)

app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog Refinement directory [options]
	Plot Euler angle distributions for refinement results. Poiont size is proportional to Euler bin count.
	>"""
	
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	
	#parser.add_pos_argument(name="plot_files",help="List the directories to plot here.", default="", guitype='filebox', browser="EMBrowserWidget(withmodal=True,multiselect=True)",  row=0, col=0,rowspan=1, colspan=2)
	parser.add_pos_argument(name="refinedir",help="The refinement directory to use for FSC plotting.", default="", guitype='dirbox', dirbasename='refine|TiltValidate',  row=0, col=0,rowspan=1, colspan=2)
	parser.add_header(name="eulerheader", help='Options below this label are specific to e2plotEuler', title="### e2plotEuler options ###", row=1, col=0, rowspan=1, colspan=1)
	parser.add_argument("--iteration",type=int,help="Refinement iteration to plot", default=0, guitype='intbox', row=2, col=0, rowspan=1, colspan=1)
	parser.add_argument("--pointwidth",type=float,help="The relative scale of the points plotted. The absoule size is dpenedent on particle count", default=1.0, guitype='floatbox', row=2, col=1, rowspan=1, colspan=1)
	parser.add_argument("--sym", dest="sym", default="c1", help="Set the symmetry; if no value is given then the model is assumed to have no symmetry.\nChoices are: i, c, d, tet, icos, or oct.", guitype='symbox', row=3, col=0, rowspan=1, colspan=2)
	parser.add_argument("--norticklabels",action="store_true",help="Disable radius tick labels", guitype='boolbox', row=4, col=0, rowspan=1, colspan=1, default=False)
	parser.add_argument("--nothetaticklabels",action="store_true",help="Disable Theta tick labels", guitype='boolbox', row=4, col=1, rowspan=1, colspan=1, default=False)
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
		
	(options, args) = parser.parse_args()

	# Grab the data
	iteration = 0
	data = EMData.read_images("bdb:%s#classify_%02d"%(args[0],iteration))
	projections = EMData.read_images("bdb:%s#projections_%02d"%(args[0],iteration))
	
	# We use a hash data structure to count same Eulers(could also use an array an sort it)
	eulerhash = {}
	for i in xrange(data[0].get_ysize()):
		# Get Eulers
		projnum = int(data[0][i])
		euler = projections[projnum].get_attr('xform.projection')
		
		#Loop over all syms
		for sym in Symmetries.get(options.sym).get_syms():
			eulerangles = (sym*euler).get_rotation('eman')
		
			# Use has to count unique eulers
			hashkey = "%3.2f %3.2f"%(eulerangles['az'],eulerangles['alt'])
			if eulerhash.has_key(hashkey):
				eulerhash[hashkey] += 1
			else:
				eulerhash[hashkey] = 1
	
	# Now plot these eulers
	theta = []
	r = []
	size = []
	for euler, count in eulerhash.items():
		eulers = euler.split()
		theta.append(float(eulers[0]))
		r.append(float(eulers[1]))
		size.append(count*options.pointwidth)
		
	# Make the QT app and plot
	app = EMApp()
	plot = EMPolarPlot2DWidget()
	plot.set_yticklabels(not options.norticklabels)
	plot.set_xticklabels(not options.nothetaticklabels)
	plot.setAxisParms(False,False)
	plot.set_data((theta,r),linewidth=50,radcut=180)
	plot.setPointSizes(size)
	plot.show()
	
	app.exec_()

# 需要导入模块: from emapplication import EMApp [as 别名]
# 或者: from emapplication.EMApp import exec_ [as 别名]
def main():
	progname = os.path.basename(sys.argv[0])
	usage = """prog Refinement directory [options]
	Plot FSC curvers produced by e2refine, eotest, etc.
	>"""
	
	parser = EMArgumentParser(usage=usage,version=EMANVERSION)
	#dirbasename='refine|frealign',
	#parser.add_pos_argument(name="plot_files",help="List the directories to plot here.", default="", guitype='filebox', browser="EMBrowserWidget(withmodal=True,multiselect=True)",  row=0, col=0,rowspan=1, colspan=2)
	parser.add_header(name="filterheader", help='There is no help', title="This program is currently not functional. The table below is still useful,\n but for actual plots, suggest using e2evalrefine.py for now.", row=0, col=0, rowspan=1, colspan=2)
	parser.add_pos_argument(name="fscdir",help="The refinement directory to use for FSC plotting.", default="", guitype='fsctable', row=1, col=0,rowspan=1, colspan=2)
	parser.add_header(name="filterheader", help='Options below this label are specific to e2plotFSC', title="### e2plotFSC options ###", row=2, col=0, rowspan=1, colspan=2)
	parser.add_argument("--plote2res",action="store_false",help="Plot curves from e2resoltion",default=True,guitype='boolbox',row=3,col=0,rowspan=1,colspan=1)
	parser.add_argument("--plote2eotest",action="store_false",help="Plot curves from e2eotest",default=True,guitype='boolbox',row=3,col=1,rowspan=1,colspan=1)
	parser.add_argument("--plotconvergence",action="store_false",help="Plot curves from refinement convergence",default=True,guitype='boolbox',row=4,col=0,rowspan=1,colspan=1)
	parser.add_argument("--ploteoconvergence",action="store_false",help="Plot curves from refine_even_odd convergence",default=True,guitype='boolbox',row=4,col=1,rowspan=1,colspan=1)
	parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
	
	(options, args) = parser.parse_args()

	# Make the QT app
	app = EMApp()
	
	# display table
	if len(args) == 0:
		fsctable = PMFSCTableWidget("fsc","",None,resize=True)
		fsctable.show()
		
	# or let user choose FSC plotting pars 
	else:
		module = EMPlot2DWidget()
	
		# Get data from data base
		db_name = "bdb:"+args[0]+"#convergence.results"
		if not db_check_dict(db_name):
			print "Rubbish!!!, no FSC curves found!!!"
			return
		db = db_open_dict(db_name,ro=True)
		keys = db.keys()
	
		# Load desired FSC curves
		res = []
		eo = []
		conv = []
		eoconv = []
		# Method to the maddness, I use not here because I need to only plot when open is not presented AND I need to keep presentation on in the GUI
		if not options.plote2res: res= get_e2resolution_results_list(keys)
		if not options.plote2eotest: eo = get_e2eotest_results_list(keys)
		if not options.plotconvergence: conv = get_convergence_results_list(keys)
		if not options.ploteoconvergence: eoconv = get_e2refine_even_odd_results_list(keys)
	
		# Plot FSC curves
		i = 0
		max = len(colortypes)		
		for k in conv:
			module.set_data(db[k],k,color=(i%max),linewidth=1) # there are only a ceratin number of  colors
			i += 1
		
		# plot e2refine_even_odd curves
		for k in eoconv:
			module.set_data(db[k],k,color=(i%max),linewidth=2) # there are only a ceratin number of  colors
			i += 1
		
		#plot eo test and res
		for plot in [eo,res]:
			for k in plot:
				module.set_data(db[k],k,color=(i%max),linewidth=3) # there are only a ceratin number of  colors
				i += 1
					
		module.show()
	app.exec_()