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)
from mien.wx.base import wx
wxapp = wx.PySimpleApp()
else:
gui=False
if files:
ma=time.time()
kwargs={'gui':gui}
if 'f' in switches:
if switches['f']=="tonmp":
kwargs["convertxml"]=True
else:
kwargs['format']=switches['f']
if 'i' in switches:
kwargs['select']=True
import mien.parsers.fileIO as io
doc=io.readall(files, **kwargs)
print time.time()-ma
else:
doc=None
if gui:
if switches.has_key('v'):
if not doc:
print "No files specified to view. Exiting"
sys.exit()
a=io.getViewerApp(doc)
if a:
switches['a']=a
if switches.has_key('a'):
app=switches['a'].lower()
if app.startswith('i'):
from mien.image.viewer import ImageViewer