def writeHeader(self, hdr):
Mrc.initHdrArrayFrom(self.fp.hdr, hdr)
self.fp.hdr.Num = hdr.Num
self.fp.hdr.PixelType = hdr.PixelType
self.fp._initWhenHdrArraySet()
if self.byteorder == '<':
self.hdr.dvid = -16224 # little_indian number
if (self.extInts is not None or self.extFloats is not None) or self.byteorder == '<':
# old ImageJ assumes that the dv format (byteorder == <) has extended header
if self.extInts is None:
self.extInts = N.zeros((1,8))
nInts = self.extInts.shape[-1]
if self.extFloats is None:
self.extFloats = N.zeros((1,32))
nFloats = self.extFloats.shape[-1]
self.fp = addExtHdrFromExt(self.fp, nInts,
nFloats, self.extInts, self.extFloats)
self.fp.hdr.NumIntegers = self.fp.extInts.shape[-1]
self.fp.hdr.NumFloats = self.fp.extFloats.shape[-1]
self.fp.setByteOrder(self.byteorder)
self.fp.writeHeader()
if hasattr(self.fp, 'extInts') or hasattr(self.fp, 'extFloats'):
self.fp.writeExtHeader(True)
self.hdr = self.fp.hdr
def writeHeader(self, hdr, extInts=None, extFloats=None, byteorder='='):
Mrc.initHdrArrayFrom(self.fp.hdr, hdr)
self.fp.hdr.Num = hdr.Num
self.fp.hdr.PixelType = hdr.PixelType
self.fp._initWhenHdrArraySet()
if extInts is not None or extFloats is not None:
if extInts is None:
extInts = N.zeros((1, 1))
if extFloats is None:
extFloats = N.zeros((1, 1))
self.fp = addExtHdrFromExt(self.fp, hdr.NumIntegers, hdr.NumFloats,
extInts, extFloats)
self.fp.hdr.NumIntegers = self.fp.extInts.shape[-1]
self.fp.hdr.NumFloats = self.fp.extFloats.shape[-1]
self.fp.setByteOrder(byteorder)
self.fp.writeHeader()
if hasattr(self.fp, 'extInts') or hasattr(self.fp, 'extFloats'):
self.fp.writeExtHeader(True)
self.hdr = self.fp.hdr
self.extInts = extInts
self.extFloats = extFloats
def makeHdr_like(hdrSrc):
"""
hdrSrc: header of the source
return header
"""
hdr = Mrc.makeHdrArray()
init_simple(hdr, hdrSrc.PixelType, hdrSrc.Num[::-1])
Mrc.initHdrArrayFrom(hdr, hdrSrc)
hdr.NumTimes = hdrSrc.NumTimes
hdr.NumWaves = hdrSrc.NumWaves
hdr.NumIntegers = hdrSrc.NumIntegers
hdr.NumFloats = hdrSrc.NumFloats
return hdr
def makeHdr_like(hdrSrc):
"""
hdrSrc: header of the source
return header
"""
hdr = Mrc.makeHdrArray()
init_simple(hdr, hdrSrc.PixelType, hdrSrc.Num[::-1])
Mrc.initHdrArrayFrom(hdr, hdrSrc)
hdr.NumTimes = hdrSrc.NumTimes
hdr.NumWaves = hdrSrc.NumWaves
hdr.NumIntegers = hdrSrc.NumIntegers
hdr.NumFloats = hdrSrc.NumFloats
return hdr
def writeHeader(self, hdr, extInts=None, extFloats=None):
Mrc.initHdrArrayFrom(self.fp.hdr, hdr)
self.fp.hdr.Num = hdr.Num
self.fp.hdr.PixelType = hdr.PixelType
self.fp._initWhenHdrArraySet()
if self.byteorder == '<':
self.hdr.dvid = -16224 # little_indian number
if (extInts is not None or extFloats is not None) or self.byteorder == '<':
# old ImageJ assumes that the dv format (byteorder == <) has extended header
if extInts is None:
extInts = N.zeros((1,8))
nInts = extInts.shape[-1]
else:
nInts = hdr.NumIntegers
if extFloats is None:
extFloats = N.zeros((1,32))
nFloats = extFloats.shape[-1]
else:
nFloats = hdr.NumFloats
self.fp = addExtHdrFromExt(self.fp, nInts,
nFloats, extInts, extFloats)
self.fp.hdr.NumIntegers = self.fp.extInts.shape[-1]
self.fp.hdr.NumFloats = self.fp.extFloats.shape[-1]
self.fp.setByteOrder(self.byteorder)
self.fp.writeHeader()
if hasattr(self.fp, 'extInts') or hasattr(self.fp, 'extFloats'):
self.fp.writeExtHeader(True)
self.hdr = self.fp.hdr
self.extInts = extInts
self.extFloats = extFloats
def alignAndCrop(self, wavelengths = [], timepoints = [],
savePath = None):
"""
Align and Crop the chosen channels/timepoints according to
values already set in this DataDoc, and save the new MRC
file result.
"""
if not wavelengths:
wavelengths = range(self.size[0])
if not timepoints:
timepoints = range(self.cropMin[1], self.cropMax[1])
# Generate the cropped shape of the file.
croppedShape = [len(wavelengths)]
for min, max in zip(self.cropMin[1:], self.cropMax[1:]):
croppedShape.append(max - min)
# Reorder to time/wavelength/z/y/x for saving.
croppedShape[0], croppedShape[1] = croppedShape[1], croppedShape[0]
croppedShape = tuple(croppedShape)
newHeader = Mrc.makeHdrArray()
Mrc.initHdrArrayFrom(newHeader, self.imageHeader)
newHeader.Num = (croppedShape[4], croppedShape[3],
croppedShape[2] * len(timepoints) * len(wavelengths))
newHeader.NumTimes = len(timepoints)
newHeader.NumWaves = len(wavelengths)
# Size of the extended header -- forced to zero for now.
newHeader.next = 0
# Ordering of data in the file; 2 means z/w/t
newHeader.ImgSequence = 2
newHeader.PixelType = Mrc.dtype2MrcMode(numpy.float32)
if not savePath:
outputArray = numpy.empty(croppedShape, numpy.float32)
else:
if self.filePath == savePath:
# \todo Why do we do this?
del self.image.Mrc
# Write out the header.
outputFile = file(savePath, 'wb')
outputFile.write(newHeader._array.tostring())
# Slices to use to crop out the 3D volume we want to use for each
# wave-timepoint pair.
volumeSlices = []
for min, max in zip(self.cropMin[2:], self.cropMax[2:]):
volumeSlices.append(slice(min, max))
for timepoint in timepoints:
for waveIndex, wavelength in enumerate(wavelengths):
volume = self.imageArray[wavelength][timepoint]
dx, dy, dz, angle, zoom = self.alignParams[wavelength]
if dz and self.size[2] == 1:
dz = 0 # in 2D files Z translation blanks out the slice!
if dx or dy or dz or angle or zoom != 1:
# Transform the volume.
volume2 = self.transformArray(
volume, dx, dy, dz, angle, zoom
)
else:
volume2 = volume.copy() # no transform
# Crop to the desired shape.
volume2 = volume2[volumeSlices].astype(numpy.float32)
if not savePath:
outputArray[timepoint, waveIndex] = volume2
else:
# Write to the file.
for i, zSlice in enumerate(volume2):
outputFile.write(zSlice)
if not savePath:
# Reorder to WTZYX since that's what the user expects.
return outputArray.transpose([1, 0, 2, 3, 4])
else:
outputFile.close()
def saveSelection(self, wavelengths = [], timepoints = [],
savePath = None):
"""
Save a wavelength=channel and/or timepoint=frame selection.
Basically a duplicate of parts of the alignAndCrop method below,
which should now be refactored to use this method instead.
Note that a new MRC object is created in the process.
"""
if not wavelengths:
wavelengths = range(self.size[0])
if not timepoints:
timepoints = range(self.cropMin[1], self.cropMax[1])
newShape = numpy.array([len(wavelengths), len(timepoints), self.size[2],
self.size[3], self.size[4] ], dtype = numpy.int)
# make a new header
newHeader = Mrc.makeHdrArray()
Mrc.initHdrArrayFrom(newHeader, self.imageHeader)
newHeader.Num = (self.size[4], self.size[3],
self.size[2] * len(timepoints) * len(wavelengths))
newHeader.NumTimes = len(timepoints)
newHeader.NumWaves = len(wavelengths)
# Size of the extended header -- forced to zero for now.
newHeader.next = 0
# Ordering of data in the file; 2 means z/w/t
newHeader.ImgSequence = 2
newHeader.PixelType = Mrc.dtype2MrcMode(numpy.float32)
if not savePath:
outputArray = numpy.empty(newShape, numpy.float32)
else:
if self.filePath == savePath:
# \todo Why do we do this?
del self.image.Mrc
# update wavelength info to ensure it remains correct
# (we could be re-ordering here)
for waveIndex, wavelength in enumerate(wavelengths):
trueWavelength = self.imageHeader.wave[wavelength]
newHeader.wave[waveIndex] = trueWavelength
# Write out the header.
outputFile = file(savePath, 'wb')
outputFile.write(newHeader._array.tostring())
for timepoint in timepoints:
for waveIndex, wavelength in enumerate(wavelengths):
volume = self.imageArray[wavelength][timepoint]
if not savePath:
outputArray[timepoint, waveIndex] = volume
else:
# Write to the file.
for i, zSlice in enumerate(volume):
outputFile.write(zSlice)
if not savePath:
# Reorder to WTZYX since that's what the user expects.
return outputArray.transpose([1, 0, 2, 3, 4])
else:
outputFile.close()