def readAndFlattenImageStack(filename):
#***********************************************
#* read imageStack and return Nx(nX*nY) array **
#***********************************************
imageStack = EMData()
imageStack.read_image(filename)
nx, ny, numImages = imageStack.get_xsize(), imageStack.get_ysize(
), imageStack.get_zsize()
imageStackData = EMNumPy.em2numpy(imageStack)
imageStack = []
#free memory
#flatten each image and append to array of NxD, with N the number of images and D the size of the flat image
imageStackData = np.reshape(imageStackData, (nx * ny, numImages),
order='F')
imageStackData = np.transpose(imageStackData)
print(imageStackData.shape)
return imageStackData
def main(args):
star = parse_star(args.input, keep_index=False)
if args.class_2d is not None:
refs = glob.glob(args.class_2d)
elif args.class_3d is not None:
refs = glob.glob(args.class_3d)
else:
refs = []
shifts = []
for r in refs:
if args.class_3d is not None:
refmap = EMData(r)
com = Vec3f(*refmap.phase_cog()[:3])
shifts.append(com)
else:
stack = EMData.read_images(r)
for im in stack:
com = Vec2f(*im.phase_cog()[:2])
shifts.append(com)
if args.class_2d is None and args.class_3d is None:
for ptcl in star.rows:
im = EMData.read_image(ptcl)
com = im.phase_cog()
ptcl["rlnOriginX"] += com[0]
ptcl["rlnOriginY"] += com[1]
else:
for ptcl in star.rows:
com = shifts[ptcl["rlnClassNumber"]]
xshift, yshift = transform_com(com, ptcl)
ptcl["rlnOriginX"] += xshift
ptcl["rlnOriginY"] += yshift
if args.zero_origin:
star["rlnCoordinateX"] = star["rlnCoordinateX"] - star["rlnOriginX"]
star["rlnCoordinateY"] = star["rlnCoordinateY"] - star["rlnOriginY"]
star["rlnOriginX"] = 0
star["rlnOriginY"] = 0
write_star(args.output, star, reindex=True)
return 0
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 get_attr_dict(self): a = EMData() a.read_image(self.file_name,self.idx,True) return a.get_attr_dict()
def write_image(self,*args): a = EMData() a.read_image(self.file_name,self.idx) a.write_image(*args)
def get_attr_dict(self):
a = EMData()
a.read_image(self.file_name, self.idx, True)
return a.get_attr_dict()
def write_image(self, *args):
a = EMData()
a.read_image(self.file_name, self.idx)
a.write_image(*args)
