def readImage(self, filename):
imagedata = None
if filename:
imagedata = self.getImageFromDB(filename)
if imagedata is None:
if filename == '':
if self.name in ['Hole Targeting','Subsquare Targeting']:
filename = os.path.join(version.getInstalledLocation(),'sq_example.jpg')
elif self.name in ['Square Targeting']:
filename = os.path.join(version.getInstalledLocation(),'gr_example.jpg')
else:
filename = os.path.join(version.getInstalledLocation(),'hl_example.jpg')
try:
orig = mrc.read(filename)
except Exception, e:
try:
orig = numpil.read(filename)
except:
self.logger.exception('Read image failed: %s' % e[-1])
return
self.currentimagedata = {'image':orig}
def readImage(self, filename):
imagedata = None
if filename:
imagedata = self.getImageFromDB(filename)
if imagedata is None:
if filename == '':
if self.name in ['Hole Targeting','Subsquare Targeting']:
filename = os.path.join(version.getInstalledLocation(),'sq_example.jpg')
elif self.name in ['Square Targeting']:
filename = os.path.join(version.getInstalledLocation(),'gr_example.jpg')
else:
filename = os.path.join(version.getInstalledLocation(),'hl_example.jpg')
try:
orig = mrc.read(filename)
except Exception, e:
try:
orig = numpil.read(filename)
except:
self.logger.exception('Read image failed: %s' % e[-1])
return
self.currentimagedata = {'image':orig}
if h['mz'] == 1:
if nframes > 1:
# mrc2014 image stack
frame_str = raw_input('This is an image stack of %d frames.\n Enter 0 to %d to select a frame to load: ' % (nframes,nframes-1))
frame = int(frame_str)
else:
if nframes > 1:
slice_str = raw_input('This is a stack of %d volume.\n Enter 0 to %d to select a slice to load: ' % (nframes,h['nz']-1))
else:
slice_str = raw_input('This is a volume.\n Enter 0 to %d to select a slice to load: ' % (h['nz']-1))
frame = int(slice_str)
image = mrc.read(filename,frame)
array = image.astype(numpy.float32)
elif filename[-4:] == '.tif':
# This is only for RawImage tiff files taken from DirectElectron DE camera
from pyami import tifffile
tif = tifffile.TIFFfile(filename)
a = tif.asarray()
a = numpy.asarray(a,dtype=numpy.float32)
# DE RawImage tiff files is mirrored horizontally from Leginon
array = a[:,::-1]
else:
from pyami import numpil
array = numpil.read(filename)
#start gui
app = MyApp(0,box)
app.panel.setImage(array)
app.MainLoop()
% (nframes, nframes - 1))
frame = int(frame_str)
else:
if nframes > 1:
slice_str = raw_input(
'This is a stack of %d volume.\n Enter 0 to %d to select a slice to load: '
% (nframes, h['nz'] - 1))
else:
slice_str = raw_input(
'This is a volume.\n Enter 0 to %d to select a slice to load: '
% (h['nz'] - 1))
frame = int(slice_str)
image = mrc.read(filename, frame)
array = image.astype(numpy.float32)
elif filename[-4:] == '.tif':
# This is only for RawImage tiff files taken from DirectElectron DE camera
from pyami import tifffile
tif = tifffile.TIFFfile(filename)
a = tif.asarray()
a = numpy.asarray(a, dtype=numpy.float32)
# DE RawImage tiff files is mirrored horizontally from Leginon
array = a[:, ::-1]
else:
from pyami import numpil
array = numpil.read(filename)
#start gui
app = MyApp(0, box)
app.panel.setImage(array)
app.MainLoop()
self.panel.setTargets('Target Practice', [])
# integration half box size
self.panel.box = box
self.sizer.Add(self.panel, 1, wx.EXPAND|wx.ALL)
frame.SetSizerAndFit(self.sizer)
self.SetTopWindow(frame)
frame.Show(True)
return True
app = MyApp(0,box)
if filename is None:
app.panel.setImage(None)
elif filename[-4:] == '.mrc':
image = mrc.read(filename)
app.panel.setImage(image.astype(numpy.float32))
elif filename[-4:] == '.tif':
# This is only for RawImage tiff files taken from DirectElectron DE camera
from pyami import tifffile
tif = tifffile.TIFFfile(filename)
a = tif.asarray()
a = numpy.asarray(a,dtype=numpy.float32)
# DE RawImage tiff files is mirrored horizontally from Leginon
a = a[:,::-1]
app.panel.setImage(a)
else:
from pyami import numpil
app.panel.setImage(numpil.read(filename))
app.MainLoop()
target=True)
self.panel.setTargets('Target Practice', [])
# integration half box size
self.panel.box = box
self.sizer.Add(self.panel, 1, wx.EXPAND | wx.ALL)
frame.SetSizerAndFit(self.sizer)
self.SetTopWindow(frame)
frame.Show(True)
return True
app = MyApp(0, box)
if filename is None:
app.panel.setImage(None)
elif filename[-4:] == '.mrc':
image = mrc.read(filename)
app.panel.setImage(image.astype(numpy.float32))
elif filename[-4:] == '.tif':
# This is only for RawImage tiff files taken from DirectElectron DE camera
from pyami import tifffile
tif = tifffile.TIFFfile(filename)
a = tif.asarray()
a = numpy.asarray(a, dtype=numpy.float32)
# DE RawImage tiff files is mirrored horizontally from Leginon
a = a[:, ::-1]
app.panel.setImage(a)
else:
from pyami import numpil
app.panel.setImage(numpil.read(filename))
app.MainLoop()
