def main():
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options]
A tool for displaying EMAN2 command history
"""
parser = EMArgumentParser(usage=usage)
parser.add_argument("--gui", "-g",default=False, action="store_true",help="Open history in an interface with a sortable table.")
parser.add_argument("--all", "-a",default=False, action="store_true",help="Show for all directories.")
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()
if options.gui:
from emapplication import EMApp
app = EMApp()
hist = HistoryForm(app,os.getcwd())
app.show()
app.execute()
else: print_to_std_out(options.all)
if not os.path.exists(file):
print("ERROR!! %s doesn't exist!\n" % file)
exit()
if __name__ == "__main__":
usage = """
sxproj_compare.py <input_imgs> <input_volume>
sxproj_compare.py <input_imgs> <input_volume> --outdir <output_directory>
sxproj_compare.py <input_imgs> <input_volume> --outdir <output_directory> --angles <angles_file>
sxproj_compare.py <input_imgs> <input_volume> --outdir <output_directory> --angles <angles_file> --select <img_selection_file>
sxproj_compare.py <input_imgs> <input_volume> --outdir <output_directory> --angles <angles_file> --select <img_selection_file> --display
"""
# Command-line arguments
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
parser.add_argument('classavgs', help='Input class averages')
parser.add_argument('vol3d', help='Input 3D reconstruction')
parser.add_argument('--outdir', "-o", type=str, help='Output directory')
parser.add_argument('--angles', "-a", type=str, help='Angles files, which will be imported into the header of the class-average stack')
parser.add_argument('--select', "-s", type=str, help='Selection file for included classes. RVIPER may exclude some images from the reconstruction.')
parser.add_argument('--display', "-d", action="store_true", help='Automatically open montage in e2display')
(options, args) = parser.parse_args()
#print args, options # (Everything is in options.)
#exit()
# If output directory not specified, write to same directory as class averages
if not options.outdir:
outdir = os.path.dirname(os.path.realpath(options.classavgs))
else:
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_()
def main():
progname = os.path.basename(sys.argv[0])
usage = """%prog [options] <image1> <image2> <image3> <image4> ....
WARNING: Experimental program. Contact [email protected] for more info.
Currently only supports bootstrapping an initial probe doing all versus all alignment of the input images
"""
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
parser.add_argument(
"--align",
type=str,
help=
"The aligner and its parameters. e.g. --align=rt.3d.grid:ralt=180:dalt=10:dphi=10:rphi=180:search=5",
default="rt.3d.grid")
parser.add_argument(
"--aligncmp",
type=str,
help="The comparator used for determing the best initial alignment",
default="dot.tomo:threshold=0")
parser.add_argument(
"--cmp",
type=str,
help="The comparator used to obtain the final similarity",
default="dot.tomo:threshold=0")
parser.add_argument(
"--ralign",
type=str,
help=
"This is the second stage aligner used to refine the first alignment. This is usually the \'refine\' aligner.",
default=None)
parser.add_argument(
"--raligncmp",
type=str,
help="The comparator used for determing the refined alignment",
default="dot.tomo:threshold=0")
parser.add_argument("--bootstrap",
action="store_true",
default=True,
help="Boot strap alignment")
parser.add_argument(
"--output",
type=str,
default="e2tomoave.hdf",
help="The output image which will store the results matrix")
parser.add_argument("--parallel",
type=str,
default=None,
help="Use parallelism")
parser.add_argument(
"--path",
default=None,
type=str,
help=
"The name of a directory where results are placed. If unspecified will generate one automatically of type tomo_ave_??."
)
parser.add_argument(
"--nsoln",
default=1,
type=int,
help=
"If supplied and greater than 1, the nsoln-best alignments will be written to a text file. This is useful for debug but may be left unspecified"
)
parser.add_argument(
"--dbls",
type=str,
help=
"data base list storage, used by the workflow. You can ignore this argument.",
default=None)
parser.add_argument(
"--shrink",
type=int,
help=
"Shrink the data as part of the alignment - for speed purposes but at the potential loss of accuracy",
default=None)
parser.add_argument(
"--filter",
type=str,
help=
"The name and parameters of an EMAN2 processor. Will be applied prior to shrinking.",
default=None)
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], higher number means higher level of verboseness")
if EMUtil.cuda_available():
parser.add_argument("--cuda",
action="store_true",
help="GPU acceleration using CUDA. Experimental",
default=False)
(options, args) = parser.parse_args()
print(options.shrink)
error_messages = check_options(options, args)
if len(error_messages) != 0:
msg = "\n"
for error in error_messages:
msg += error + "\n"
parser.error(msg)
exit(1)
logger = E2init(sys.argv, options.ppid)
if options.bootstrap:
module = EMBootStrappedAverages(args, options, logger)
module.execute()
else:
print("boot strap only supported technique")
E2end(logger)
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options]
A tool for displaying EMAN2 command history
"""
parser = EMArgumentParser(usage=usage)
parser.add_argument(
"--gui",
"-g",
default=False,
action="store_true",
help="Open history in an interface with a sortable table.")
parser.add_argument("--all",
"-a",
default=False,
action="store_true",
help="Show for all directories.")
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()
if options.gui:
from eman2_gui.emapplication import EMApp
app = EMApp()
hist = HistoryForm(app, os.getcwd())
hist.form.show()
hist.form.raise_()
app.show()
app.execute()
else:
print_to_std_out(options.all)
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(
"--hist",
action="store_true",
default=False,
help=
"Data file(s) should be plotted as a histogram rather than displayed in 2-D."
)
parser.add_argument(
"--plot3d",
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], higher number means higher level of verboseness")
(options, args) = parser.parse_args()
# logid=E2init(sys.argv)
app = EMApp()
#gapp = app
#QtWidgets.QApplication(sys.argv)
win = []
if options.fullrange:
print(
"""The --fullrange option has been removed, and replaced with an option in user preferences.
To set your preferences for full-range 2-D display, please run:
e2procjson.py --setoption display2d.autocontrast:true
""")
sys.exit(0)
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.hist:
hist(args, app)
elif options.plot3d:
plot_3d(args, app)
elif options.classes:
options.classes = options.classes.split(",")
imgs = EMData.read_images(args[0])
display(imgs, app, args[0])
win[0].child.mousedown.connect(lambda a, b: selectclass(
options.classes[0], options.classes[1], a, b))
try:
out = open("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)
app.exec_()
Updates StarFile entry to match MetaData instance.
Beware: ONLY UPDATES FIELDS MODIFIED ELSEWHERE IN THIS PROGRAM!
:param self: The MetaData object.
:param star: StarFile object with matching indices
:return: None
"""
star['rlnOriginX'][self.i] = self.x_origin
star['rlnOriginY'][self.i] = self.y_origin
MetaData.update = update # Monkey patch the MetaData class.
if __name__ == "__main__":
usage = "projection_subtraction.py [options] output_suffix"
parser = EMArgumentParser(usage=usage,
version="projection_subtraction.py 1.0a, " +
EMANVERSION)
parser.add_argument(
"--input",
type=str,
help="RELION .star file listing input particle image stack(s)")
parser.add_argument(
"--wholemap",
type=str,
help="Map used to calculate projections for normalization")
parser.add_argument("--submap",
type=str,
help="Map used to calculate subtracted projections")
parser.add_argument(
"--output",
type=str,
counter = 0
# Loop through classes
with open(classmap) as r:
for idx, line in enumerate(r.readlines()):
with open(classdoc.format(idx), 'w') as w:
w.write('\n'.join(line[1:-3].split(', ')))
counter += 1
print_log_msg("Wrote %s class selection files\n" % counter, log, verbose)
if __name__ == "__main__":
# Command-line arguments
parser = EMArgumentParser(usage=USAGE, version=EMANVERSION)
parser.add_argument('classavgs', help='Input class averages')
parser.add_argument('instack', help='Input image stack')
parser.add_argument('outdir', type=str, help='Output directory')
parser.add_argument(
'--filtrad',
type=float,
help=
'For optional filtered images, low-pass filter radius (1/px or, if pixel size specified, Angstroms)'
)
parser.add_argument(
'--pxsz',
type=float,
default=None,
help='Pixel size, Angstroms (might be downsampled by ISAC)')
parser.add_argument('--shrink',
def main(): progname = os.path.basename(sys.argv[0]) usage = """%prog [options] <image1> <image2> <image3> <image4> .... WARNING: Experimental program. Contact [email protected] for more info. Currently only supports bootstrapping an initial probe doing all versus all alignment of the input images """ parser = EMArgumentParser(usage=usage,version=EMANVERSION) parser.add_argument("--align",type=str,help="The aligner and its parameters. e.g. --align=rt.3d.grid:ralt=180:dalt=10:dphi=10:rphi=180:search=5", default="rt.3d.grid") parser.add_argument("--aligncmp",type=str,help="The comparator used for determing the best initial alignment", default="dot.tomo:threshold=0") parser.add_argument("--cmp",type=str,help="The comparator used to obtain the final similarity", default="dot.tomo:threshold=0") parser.add_argument("--ralign",type=str,help="This is the second stage aligner used to refine the first alignment. This is usually the \'refine\' aligner.", default=None) parser.add_argument("--raligncmp",type=str,help="The comparator used for determing the refined alignment", default="dot.tomo:threshold=0") parser.add_argument("--bootstrap",action="store_true",default=True,help="Boot strap alignment") parser.add_argument("--output",type=str,default="e2tomoave.hdf",help="The output image which will store the results matrix") parser.add_argument("--parallel",type=str,default=None,help="Use parallelism") parser.add_argument("--path", default=None, type=str,help="The name of a directory where results are placed. If unspecified will generate one automatically of type tomo_ave_??.") parser.add_argument("--nsoln", default=1, type=int,help="If supplied and greater than 1, the nsoln-best alignments will be written to a text file. This is useful for debug but may be left unspecified") parser.add_argument("--dbls",type=str,help="data base list storage, used by the workflow. You can ignore this argument.",default=None) parser.add_argument("--shrink",type=int,help="Shrink the data as part of the alignment - for speed purposes but at the potential loss of accuracy",default=None) parser.add_argument("--filter",type=str,help="The name and parameters of an EMAN2 processor. Will be applied prior to shrinking.",default=None) 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") if EMUtil.cuda_available(): parser.add_argument("--cuda",action="store_true",help="GPU acceleration using CUDA. Experimental", default=False) (options, args) = parser.parse_args() print options.shrink error_messages = check_options(options,args) if len(error_messages) != 0: msg = "\n" for error in error_messages: msg += error +"\n" parser.error(msg) exit(1) logger=E2init(sys.argv,options.ppid) if options.bootstrap: module = EMBootStrappedAverages(args,options,logger) module.execute() else: print "boot strap only supported technique" E2end(logger)
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("--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=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,
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=4.0,
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("--write_dbbox",
action="store_true",
help="Write coordinate file (eman1 dbbox) files",
default=False,
guitype='boolbox',
row=3,
col=0,
rowspan=1,
colspan=1,
mode="extraction")
parser.add_argument("--write_ptcls",
action="store_true",
help="Write particles to disk",
default=False,
guitype='boolbox',
row=3,
col=1,
rowspan=1,
colspan=1,
mode="extraction[True]")
parser.add_argument("--invert",
action="store_true",
help="If writing outputt inverts pixel intensities",
default=False,
guitype='boolbox',
row=3,
col=2,
rowspan=1,
colspan=1,
mode="extraction")
parser.add_argument(
"--ppid",
type=int,
help="Set the PID of the parent process, used for cross platform PPID",
default=-1)
parser.add_argument("--gui",
action="store_true",
default=True,
help="Dummy option; used in older version of e2boxer")
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()
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("--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=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, 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=4.0, 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("--write_dbbox",action="store_true",help="Write coordinate file (eman1 dbbox) files",default=False, guitype='boolbox', row=3, col=0, rowspan=1, colspan=1, mode="extraction")
parser.add_argument("--write_ptcls",action="store_true",help="Write particles to disk",default=False, guitype='boolbox', row=3, col=1, rowspan=1, colspan=1, mode="extraction[True]")
parser.add_argument("--invert",action="store_true",help="If writing outputt inverts pixel intensities",default=False, guitype='boolbox', row=3, col=2, rowspan=1, colspan=1, mode="extraction")
parser.add_argument("--ppid", type=int, help="Set the PID of the parent process, used for cross platform PPID",default=-1)
parser.add_argument("--gui", action="store_true", default=True, help="Dummy option; used in older version of e2boxer")
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()
