DM_r_convert.py

## @package python.demo.DM_r_convert
# 
# converting points into an R data frame objects
# 
 
from __future__ import print_function  # print function syntax as in python 3
import rpy2.robjects as robjects
import sys
 
##raw_input("start debugger")
 
from opals import pyDM
 
 
def DM_r_convert(filename):
    # open the odm / pyDM.Datamanager.load parameters: filename(string), readOnly(bool) threadSafety(bool)
    dm = pyDM.Datamanager.load(filename, True, False)
 
    # if the dm wasn't opened sucessful exit function
    if not dm:
        print("Unable to open ODM '" + filename + "'")
        return
 
    # create a layout for conversion
    f = pyDM.AddInfoLayoutFactory()
    f.addColumn(pyDM.ColumnSemantic.Amplitude)  # pre-defined attribute "Amplitude"
    f.addColumn(pyDM.ColumnSemantic.EchoWidth)  # pre-defined attribute "EchoWidth"
    layout = f.getLayout()
 
    pi = dm.getPointIndex()
 
    # convert each leaf into a data frame
    dfs = []
    for leaf in pi.leafs():
        # get the leaf as r data frame
        df = leaf.asRDataFrame(layout, True)
 
        # append df object to list
        dfs.append(df)
 
    # create a single data frame
    idx = 0
    df = pyDM.RConverter.createDataFrame(pi.sizePoint(), layout, True)
    for leaf in pi.leafs():
        pyDM.RConverter.fillDataFrame(df, idx, leaf)
        idx += leaf.sizePoint()
 
 
if len(sys.argv) == 1:
    print("ODM parameter missing")
    sys.exit(-1)
 
DM_r_convert(sys.argv[1])
 
print("finished")