def validate_file_name(self,file_name):
'''
Validate the file name and do any internal preparation for the impending call to
save.
Checks to make sure the file name is valid
Confirms overwrite and asks to append
@return 0 if something went wrong (e.g. the user cancelled), 1 if it's okay to call save now
'''
msg = QtGui.QMessageBox()
error = self.__validate_file_name(file_name)
if error != None:
# error is therefore a string
msg.setText(error)
msg.exec_()
return 0
# If we make it here the file name is fine, but it may exist
self.overwrite = False
self.append = False
if file_exists(file_name):
file_exists_dialog = EMFileExistsDialog(file_name,self.__item_list)
code = file_exists_dialog.exec_()
if code == 0:
return 0
elif code == 1:
self.overwrite = True
elif code == 2:
self.append = True
else: raise NotImplementedError("A developer has modified the code and this has caused an error. Please notify us")
return 1
def validate_file_name(self,file_name):
'''
Validate the file name and do any internal preparation for the impending call to
save.
Checks to make sure the file name is valid
Confirms overwrite and asks to append
@return 0 if something went wrong (e.g. the user cancelled), 1 if it's okay to call save now
'''
msg = QtGui.QMessageBox()
error = self.__validate_file_name(file_name)
if error != None:
# error is therefore a string
msg.setText(error)
msg.exec_()
return 0
# If we make it here the file name is fine, but it may exist
self.overwrite = False
self.append = False
if file_exists(file_name):
file_exists_dialog = EMFileExistsDialog(file_name,self.__item_list)
code = file_exists_dialog.exec_()
if code == 0:
return 0
elif code == 1:
self.overwrite = True
elif code == 2:
self.append = True
else: raise NotImplementedError("A developer has modified the code and this has caused an error. Please notify us")
return 1
def __init__(self,file_name,idx=0):
'''
@exception RuntimeError raised if the file_name does not exist
'''
if not file_exists(file_name): raise RuntimeError("%s does not exist" %file_name)
self.file_name = file_name
self.idx = idx
def __init__(self,file_name,idx=0):
'''
@exception RuntimeError raised if the file_name does not exist
'''
if not file_exists(file_name): raise RuntimeError("%s does not exist" %file_name)
self.file_name = file_name
self.idx = idx
def __new__(cls, file_name):
if not file_exists(file_name): raise
splt = file_name.split(".")
if len(file_name) > 4 and file_name[:4] == "bdb:": pass
elif EMUtil.get_image_ext_type(splt[-1]) == EMUtil.ImageType.IMAGE_UNKNOWN:
raise
if splt[-1] in ["img","hed"]: return EMImagicTmpFileHandle(file_name)
elif file_name[:4] == "bdb:": return EMDBTmpFileHandle(file_name)
else: return EMGeneralTmpFileHandle(file_name)
def __new__(cls, file_name):
if not file_exists(file_name): raise
splt = file_name.split(".")
if len(file_name) > 4 and file_name[:4] == "bdb:": pass
elif EMUtil.get_image_ext_type(splt[-1]) == EMUtil.ImageType.IMAGE_UNKNOWN:
raise
if splt[-1] in ["img","hed"]: return EMImagicTmpFileHandle(file_name)
elif file_name[:4] == "bdb:": return EMDBTmpFileHandle(file_name)
else: return EMGeneralTmpFileHandle(file_name)
def display(img,app,title="EMAN2 image"): if len(img)==1 : img=img[0] w=EMImageWidget(data=img,old=None,app=app) w.setWindowTitle(title) try: if file_exists(title): w.set_file_name(title) except: pass app.show_specific(w) try: w.optimally_resize() except: pass return w
def display(img,app,title="EMAN2 image"): if len(img)==1 : img=img[0] w=EMImageWidget(data=img,old=None,app=app) w.setWindowTitle(title) try: if file_exists(title): w.set_file_name(title) except: pass app.show_specific(w) try: w.optimally_resize() except: pass return w
def check_options(options,args):
'''
A way to check the options, arg as returned by parser.parse_args() in e2tomoaverage
'''
error = []
error.extend(check_tomo_options(options)) # there is a big bunch of generic options
if len(args) < 2:
error.append("Error - to average you must supply atleast two images")
else:
for arg in args:
if not file_exists(arg):
error.append("%s does not exist" %arg)
if options.path != None:
if not os.path.exists(options.path):
error.append( "Error: the path %s does not exist" %options.path)
else:
options.path = EMAN2.numbered_path(tomo_ave_path_root,True)
return error
def __new__(cls,filename,application,force_plot=False,force_2d=False,old=None):
file_type = Util.get_filename_ext(filename)
em_file_type = EMUtil.get_image_ext_type(file_type)
if not file_exists(filename): return None
if force_plot and force_2d:
# ok this sucks but it suffices for the time being
print "Error, the force_plot and force_2d options are mutually exclusive"
return None
if force_plot:
from emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
if em_file_type != IMAGE_UNKNOWN or filename[:4] == "bdb:":
n = EMUtil.get_image_count(filename)
nx,ny,nz = gimme_image_dimensions3D(filename)
if n > 1 and nz == 1:
if force_2d:
a = EMData()
data=a.read_images(filename)
else:
data = None # This is like a flag - the ImageMXWidget only needs the file name
elif nz == 1:
data = [EMData(filename,0)]
else:
data = EMData()
data.read_image(filename,0,not force_2d) # This should be 3-D. We read the header-only here
data = [data]
if data != None and len(data) == 1: data = data[0]
if force_2d or isinstance(data,EMData) and data.get_zsize()==1:
if isinstance(data,list) or data.get_ysize() != 1:
from emimage2d import EMImage2DWidget
if isinstance(old,EMImage2DWidget): widget = old
else: widget= EMImage2DWidget(application=application)
else:
from emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
elif isinstance(data,EMData):
if isinstance(old,EMScene3D): widget = old
else: widget = EMScene3D()
# print n,data
for ii in xrange(n):
data=EMData(filename,ii)
datai = EMDataItem3D(data, transform=Transform())
widget.insertNewNode(os.path.basename(filename), datai, parentnode=widget)
isosurface = EMIsosurface(datai, transform=Transform())
widget.insertNewNode("Iso", isosurface, parentnode=datai)
return widget
elif data == None or isinstance(data,list):
from emimagemx import EMImageMXWidget
if isinstance(old,EMImageMXWidget): widget = old
else: widget = EMImageMXWidget(application=application)
data = filename
else:
print filename
raise # weirdness, this should never happen
widget.set_data(data,filename)
return widget
else:
from emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
def __new__(cls,filename,application,force_plot=False,force_2d=False,old=None):
file_type = Util.get_filename_ext(filename)
em_file_type = EMUtil.get_image_ext_type(file_type)
if not file_exists(filename): return None
if force_plot and force_2d:
# ok this sucks but it suffices for the time being
print("Error, the force_plot and force_2d options are mutually exclusive")
return None
if force_plot:
from .emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
if em_file_type != IMAGE_UNKNOWN or filename[:4] == "bdb:":
n = EMUtil.get_image_count(filename)
nx,ny,nz = gimme_image_dimensions3D(filename)
if n > 1 and nz == 1:
if force_2d:
a = EMData()
data=a.read_images(filename)
else:
data = None # This is like a flag - the ImageMXWidget only needs the file name
elif nz == 1:
data = [EMData(filename,0)]
else:
data = EMData()
data.read_image(filename,0,not force_2d) # This should be 3-D. We read the header-only here
data = [data]
if data != None and len(data) == 1: data = data[0]
if force_2d or isinstance(data,EMData) and data.get_zsize()==1:
if isinstance(data,list) or data.get_ysize() != 1:
from .emimage2d import EMImage2DWidget
if isinstance(old,EMImage2DWidget): widget = old
else: widget= EMImage2DWidget(application=application)
else:
from .emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
elif isinstance(data,EMData):
if isinstance(old,EMScene3D): widget = old
else: widget = EMScene3D()
# print n,data
for ii in range(n):
data=EMData(filename,ii)
datai = EMDataItem3D(data, transform=Transform())
widget.insertNewNode(os.path.basename(filename), datai, parentnode=widget)
isosurface = EMIsosurface(datai, transform=Transform())
widget.insertNewNode("Iso", isosurface, parentnode=datai)
return widget
elif data == None or isinstance(data,list):
from .emimagemx import EMImageMXWidget
if isinstance(old,EMImageMXWidget): widget = old
else: widget = EMImageMXWidget(application=application)
data = filename
else:
print(filename)
raise # weirdness, this should never happen
widget.set_data(data,filename)
return widget
else:
from .emplot2d import EMPlot2DWidget
if isinstance(old,EMPlot2DWidget): widget = old
else: widget = EMPlot2DWidget(application=application)
widget.set_data_from_file(filename)
return widget
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] <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_()
