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