def saveNewMrc(mrc_path, arr, n_tzcyx, cal_xyz, wavelengths=None):
"""
Write a new Mrc file using numpy ndarray 'arr' and tuples of
- dimension sizes (nt, nz, nc, ny, nx) and
- float pixel calibrations in microns (cal_x, cal_y, cal_z)
"""
nt, nz, nc, ny, nx = n_tzcyx
if not wavelengths:
wavelengths = tuple(900 + n for n in range(5))
arr = numpy.reshape(arr, n_tzcyx) # introduce length 1 dimensions
arr = arr.transpose([0, 2, 1, 3, 4]) # Mrc output shape "ZWT"
hdr = Mrc.makeHdrArray()
mrc_mode = Mrc.dtype2MrcMode(arr.dtype)
nslices = nt * nz * nc
Mrc.init_simple(hdr, mrc_mode, (nslices, ny, nx)) # set default hdr values
hdr.NumTimes = nt
hdr.NumWaves = nc
hdr.ImgSequence = 2 # write in order "ZWT"
hdr.d = cal_xyz
hdr.wave = wavelengths
# write header & slices
f_out = file(mrc_path, 'wb')
f_out.write(hdr._array.tostring())
for t in range(nt):
for c in range(nc):
for z in range(nz):
arr_yx_yinverted = arr[t, c, z, ::-1, :]
f_out.write(arr_yx_yinverted.copy(order='C'))
f_out.close()
return DataDoc(mrc_path)
def makeHdrFromRdr(rdr):
"""
rdr: reader object
return header
"""
if hasattr(rdr, 'hdr'):
hdr = rdr.hdr
else:
hdr = Mrc.makeHdrArray()
Mrc.init_simple(hdr, Mrc.dtype2MrcMode(rdr.dtype), rdr.shape)
hdr.ImgSequence = rdr.imgSequence
hdr.NumTimes = rdr.nt
hdr.NumWaves = rdr.nw
hdr.Num[-1] = rdr.nt * rdr.nw * rdr.nz
if len(rdr.wave):
if [
1 for wave in rdr.wave[:rdr.nw]
if isinstance(wave, basestring)
]:
hdr.wave[:rdr.nw] = 0
else:
hdr.wave[:rdr.nw] = rdr.wave[:rdr.nw]
hdr.d = rdr.pxlsiz[::-1]
if rdr.metadata.has_key('Instrument'):
hdr.LensNum = eval(
rdr.metadata['Instrument']['Objective']['ID'].split(':')[1])
return hdr
def makeHdr(self):
"""
make a Mrc header using the available dimension information to export
"""
if not self.hdr:
hdr = Mrc.makeHdrArray()
Mrc.init_simple(hdr, Mrc.dtype2MrcMode(self.dtype), self.shape)
hdr.ImgSequence = self.imgSequence
hdr.NumTimes = self.nt
hdr.NumWaves = self.nw
hdr.Num[-1] = self.nt * self.nw * self.nz
if len(self.wave):
hdr.wave[:self.nw] = self.wave[:self.nw]
hdr.d = self.pxlsiz[::-1]
if 'Instrument' in self.metadata:
hdr.hdr.LensNum = eval(self.metadata['Instrument']['Objective']['ID'].split(':')[1])
self.hdr = hdr
def makeHdr(self):
"""
make a Mrc header using the available dimension information to export
"""
if not self.hdr:
hdr = Mrc.makeHdrArray()
Mrc.init_simple(hdr, Mrc.dtype2MrcMode(self.dtype), self.shape)
hdr.ImgSequence = self.imgSequence
hdr.NumTimes = self.nt
hdr.NumWaves = self.nw
hdr.Num[-1] = self.nt * self.nw * self.nz
if len(self.wave):
hdr.wave[:self.nw] = self.wave[:self.nw]
hdr.d = self.pxlsiz[::-1]
if 'Instrument' in self.metadata:
hdr.hdr.LensNum = eval(self.metadata['Instrument']['Objective']['ID'].split(':')[1])
self.hdr = hdr
def makeHdrFromRdr(rdr):
"""
rdr: reader object
return header
"""
if hasattr(rdr, 'hdr'):
hdr = makeHdr_like(rdr.hdr)
else:
hdr = Mrc.makeHdrArray()
Mrc.init_simple(hdr, Mrc.dtype2MrcMode(rdr.dtype), rdr.shape)
hdr.ImgSequence = rdr.imgSequence
hdr.NumTimes = rdr.nt
hdr.NumWaves = rdr.nw
hdr.Num[-1] = rdr.nt * rdr.nw * rdr.nz
if len(rdr.wave):
if [1 for wave in rdr.wave[:rdr.nw] if isinstance(wave, six.string_types)]:
hdr.wave[:rdr.nw] = 0
else:
hdr.wave[:rdr.nw] = rdr.wave[:rdr.nw]
hdr.d = rdr.pxlsiz[::-1]
if 'Instrument' in rdr.metadata:
hdr.LensNum = eval(rdr.metadata['Instrument']['Objective']['ID'].split(':')[1])
return hdr