def makeFilesForETomoSampleRecon(processdir, stackdir,aligndir, templatedir, seriesname, thickness, pixelsize,yspacing,has_rotation=False):
'''
Make or link local files required by etomo to redo sampling, creating tomopitch model, and reconstruct the volume.
'''
# etomo status file
createETomoBoundaryModelEDF(processdir,templatedir,seriesname,thickness,pixelsize)
# required by remaking sample tomograms inside etomo
if has_rotation:
apDisplay.printWarning('eTomo wants to regenerate global alignment from non-rotated local alignment. This alignment with rotation will not work right')
else:
# prexf file is generated from database values if this function is called from tomomaker. It is better not to change it if exists.
prexf = seriesname+".prexf"
alignprexf = os.path.join(aligndir,prexf)
localprexf = os.path.join(processdir,prexf)
apFile.safeCopy(alignprexf,localprexf)
writeETomoNewstComTemplate(processdir, seriesname)
rawtltname = '%s.rawtlt' % (seriesname)
shutil.copy(os.path.join(stackdir,rawtltname),os.path.join(processdir,rawtltname))
# required by tomopitch model making
tomopitchname = 'tomopitch.com'
imodcomdir = os.path.join(os.environ['IMOD_DIR'],'com')
tomopitchpath = os.path.join(processdir,tomopitchname)
shutil.copy(os.path.join(imodcomdir,tomopitchname),tomopitchpath)
apFile.replaceUniqueLinePatternInTxtFile(tomopitchpath,'SpacingInY','SpacingInY\t%.1f\n' % yspacing)
# required by "Final Aligned Stack" step
stackname = '%s.st' % (seriesname)
apFile.safeSymLink(os.path.join(stackdir,stackname),os.path.join(processdir,stackname))
def makeFilesForETomoSampleRecon(processdir,
stackdir,
aligndir,
templatedir,
seriesname,
thickness,
pixelsize,
yspacing,
has_rotation=False):
'''
Make or link local files required by etomo to redo sampling, creating tomopitch model, and reconstruct the volume.
'''
# etomo status file
createETomoBoundaryModelEDF(processdir, templatedir, seriesname, thickness,
pixelsize)
# required by remaking sample tomograms inside etomo
if has_rotation:
apDisplay.printWarning(
'eTomo wants to regenerate global alignment from non-rotated local alignment. This alignment with rotation will not work right'
)
else:
# prexf file is generated from database values if this function is called from tomomaker. It is better not to change it if exists.
prexf = seriesname + ".prexf"
alignprexf = os.path.join(aligndir, prexf)
localprexf = os.path.join(processdir, prexf)
apFile.safeCopy(alignprexf, localprexf)
writeETomoNewstComTemplate(processdir, seriesname)
rawtltname = '%s.rawtlt' % (seriesname)
shutil.copy(os.path.join(stackdir, rawtltname),
os.path.join(processdir, rawtltname))
# required by tomopitch model making
tomopitchname = 'tomopitch.com'
imodcomdir = os.path.join(os.environ['IMOD_DIR'], 'com')
tomopitchpath = os.path.join(processdir, tomopitchname)
shutil.copy(os.path.join(imodcomdir, tomopitchname), tomopitchpath)
apFile.replaceUniqueLinePatternInTxtFile(tomopitchpath, 'SpacingInY',
'SpacingInY\t%.1f\n' % yspacing)
# required by "Final Aligned Stack" step
stackname = '%s.st' % (seriesname)
apFile.safeSymLink(os.path.join(stackdir, stackname),
os.path.join(processdir, stackname))
def linkStackRawtltFiles(stackdir, processdir, seriesname):
for ext in ('st', 'rawtlt'):
filename = seriesname + '.' + ext
source = os.path.join(stackdir, filename)
destination = os.path.join(processdir, filename)
apFile.safeSymLink(source, destination)
def linkStackRawtltFiles(stackdir,processdir,seriesname):
for ext in ('st','rawtlt'):
filename = seriesname+'.'+ext
source = os.path.join(stackdir,filename)
destination = os.path.join(processdir,filename)
apFile.safeSymLink(source, destination)
