def __init__(self):
QtGui.QWidget.__init__(self)
self.widget = EMScene3D()
self.cube1 = EMCube(50.0)
self.widget.insertNewNode("Cube1", self.cube1) # Something to Render something..... an EMItem3D
self.cube2 = EMCube(50.0)
self.widget.insertNewNode("Cube2", self.cube2)
self.sphere = EMSphere(50.0)
self.widget.insertNewNode("Sphere", self.sphere)
self.cylinder = EMCylinder(50, 300)
self.widget.insertNewNode("Cylinder", self.cylinder)
self.cone = EMCone(50, 300)
self.widget.insertNewNode("Cone", self.cone)
self.line = EMLine(10,10,10,200,200,200, 16)
self.widget.insertNewNode("Line", self.line)
self.text1 = EM3DText('3D text', 75)
self.widget.insertNewNode("Text1", self.text1)
#Show inspector
#self.widget.showInspector()
# QT stuff to display the widget
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.widget)
self.setLayout(vbox)
self.setGeometry(300, 300, 600, 600)
self.setWindowTitle('BCM EM Viewer')
def load_pdb(files, app):
from empdbitem3D import EMPDBItem3D, EMBallStickModel
scene = EMScene3D()
title = []
for f in files:
pdb_model = EMPDBItem3D(f)
scene.insertNewNode(f.split("/")[-1], pdb_model)
modeltype = EMBallStickModel(f)
scene.insertNewNode(modeltype.representation,
modeltype,
parentnode=pdb_model)
scene.addChild(EMPDBItem3D(f))
title.append(pdb_model.getName())
scene.setWindowTitle(" ".join(title))
scene.show()
return scene
def main():
progname = os.path.basename(sys.argv[0])
usage = """e2pdbviewer.py <project directory>
A wrapper program to view a .pdb file on your computer. This is simply an PDB
specific interface to the more general EMScene3D viewer.
"""
parser = EMArgumentParser(usage=usage, version=EMANVERSION)
parser.add_argument("--pdbfiles",
type=str,
help="Specify one or mode pdb files you \
wish to view",
nargs='*',
required=False,
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" )
(options, args) = parser.parse_args()
logid = E2init(sys.argv, options.ppid)
app = EMApp()
viewer = EMScene3D()
if options.pdbfiles:
models = [
EMStructureItem3D(pdb_file=pdbf) for pdbf in options.pdbfiles
]
viewer.addChildren(models)
viewer.show()
app.execute()
E2end(logid)
def setData(self, data):
if data == None:
self.data = None
return
elif isinstance(data, str):
self.datafile = data
self.nimg = EMUtil.get_image_count(data)
self.origdata = EMData(data, 0)
if self.origdata["nz"] == 1:
if self.nimg > 20:
self.origdata = EMData.read_images(
data, range(0, self.nimg, self.nimg / 20)
) # read regularly separated images from the file totalling ~20
elif self.nimg > 1:
self.origdata = EMData.read_images(data, range(self.nimg))
else:
self.origdata = [self.origdata]
else:
self.origdata = [self.origdata]
else:
self.datafile = None
if isinstance(data, EMData): self.origdata = [data]
else: self.origdata = data
self.nx = self.origdata[0]["nx"]
self.ny = self.origdata[0]["ny"]
self.nz = self.origdata[0]["nz"]
if self.apix <= 0.0: self.apix = self.origdata[0]["apix_x"]
EMProcessorWidget.parmdefault["apix"] = (0, (0.2, 10.0), self.apix,
None)
origfft = self.origdata[0].do_fft()
self.pspecorig = origfft.calc_radial_dist(self.ny / 2, 0.0, 1.0, 1)
ds = 1.0 / (self.apix * self.ny)
self.pspecs = [ds * i for i in range(len(self.pspecorig))]
if self.viewer != None:
for v in self.viewer:
v.close()
if self.nz == 1 or self.force2d:
if len(self.origdata) > 1:
self.viewer = [EMImageMXWidget()]
self.mfile_save_stack.setEnabled(True)
self.mfile_save_map.setEnabled(False)
else:
self.viewer = [EMImage2DWidget()]
self.mfile_save_stack.setEnabled(False)
self.mfile_save_map.setEnabled(True)
else:
self.mfile_save_stack.setEnabled(False)
self.mfile_save_map.setEnabled(True)
self.viewer = [EMScene3D()]
self.sgdata = EMDataItem3D(test_image_3d(3), transform=Transform())
self.viewer[0].insertNewNode('Data',
self.sgdata,
parentnode=self.viewer[0])
isosurface = EMIsosurface(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Iso",
isosurface,
parentnode=self.sgdata)
volslice = EMSliceItem3D(self.sgdata, transform=Transform())
self.viewer[0].insertNewNode("Slice",
volslice,
parentnode=self.sgdata)
E2loadappwin("e2filtertool", "image", self.viewer[0].qt_parent)
self.procChange(-1)
def __new__(cls,
data=None,
old=None,
app=None,
force_2d=False,
force_plot=False,
filename="",
replace=True):
"""This will create a new EMImage* object depending on the type of 'data'. If
old= is provided, and of the appropriate type, it will be used rather than creating
a new instance.
"""
if isinstance(data, EMData) and data.get_size() == 0:
raise RuntimeError(
"Can not display an EMData object that has no pixels")
from EMAN2 import remove_directories_from_name
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 or (isinstance(data, EMData) and data.get_zsize() == 1
and data.get_ysize() == 1):
from emplot2d import EMPlot2DWidget
if old:
if isinstance(old, EMPlot2DWidget):
old.set_data(data, remove_directories_from_name(filename),
replace)
return old
widget = EMPlot2DWidget(application=app)
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
elif force_2d or (isinstance(data, EMData) and data.get_zsize() == 1):
from emimage2d import EMImage2DWidget
if old:
if isinstance(old, EMImage2DWidget):
old.set_data(data, filename)
return old
widget = EMImage2DWidget(application=app)
widget.set_data(data, filename)
return widget
elif isinstance(data, EMData):
if isinstance(old, EMScene3D): widget = old
else: widget = EMScene3D()
data = EMDataItem3D(data, transform=Transform())
#data.setSelectedItem(True)
isosurface = EMIsosurface(data, transform=Transform())
widget.insertNewNode(os.path.basename(filename),
data,
parentnode=widget)
widget.insertNewNode("Iso", isosurface, parentnode=data)
return widget
elif isinstance(data, list) and isinstance(data[0], EMData):
from emimagemx import EMImageMXWidget
if old:
if isinstance(old, EMImageMXWidget):
old.set_data(data, filename)
return old
widget = EMImageMXWidget(application=app)
widget.set_data(data, filename)
return widget
elif isinstance(data, list):
from emplot3d import EMPlot3DWidgetNew
if (isinstance(data[0], list)
or isinstance(data[0], tuple)) and len(data) > 2:
if old:
if isinstance(old, EMPlot3DWidgetNew):
old.set_data(data,
remove_directories_from_name(filename),
replace)
return old
widget = EMPlot3DWidgetNew()
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
else:
from emplot2d import EMPlot2DWidget
if old:
if isinstance(old, EMPlot2DWidget):
old.set_data(data,
remove_directories_from_name(filename),
replace)
return old
widget = EMPlot2DWidget(application=app)
widget.set_data(data, remove_directories_from_name(filename),
replace)
return widget
else:
raise Exception(
"data must be a single EMData object or a list of EMData objects"
)
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