def pts2data(arg):
"""pts2data fname [fname2 [...]] - extract points from sphere fiducials to a text data file
This function will load the contents of all the named files (provided they are readable by MIEN),
select all the Fiducial elements that have Style == spheres, extract the point data from these
elements, concatenate the data into a single data element, and print that data to standard output
in text data file format. You can use shell redirection (e.g. "pts2data fname > data.txt") to
write the points to a file.
"""
doc = io.readall(arg)
fid = doc.getElements("Fiducial", {"Style": "spheres"})
pts = [f.getPoints() for f in fid]
pts = row_stack(pts)
d = md.newData(pts, {"SampleType": "generic"})
f = io.match_extension("txt")[0]
io.write(d, sys.stdout, format=f, newdoc=True)
else:
import mien.interface.cli as cli
if switches.has_key('t'):
cli.startCli(doc)
elif switches.has_key('s'):
cli.scan(doc, int(switches['s']))
elif switches.has_key('r'):
from mien.interface.cli import runmethod
runmethod(doc, switches['r'])
elif switches.has_key('c'):
format=switches['c']
if not io.filetypes.has_key(format):
try:
if not format.startswith('.'):
format='.'+format
format=io.match_extension(format)[0]
except:
print "Can't determine format (use mien -f list to see formats)"
format=None
if format:
fname, ex=os.path.splitext(files[0])
ex=ex[1:]
if ex.isdigit():
fname=fname+"-"+ex
ma=time.time()
io.write(doc, fname, format=format, forceext=True)
print time.time()-ma
sys.exit()
