view eden_wrapper.py @ 0:95a776023fbc draft

Uploaded

#!/usr/bin/env python
import argparse
import sys
import os
import subprocess
import random
import tempfile
import shlex
import shutil
from eden_utilities import log

class EDeNWrapper:
    
    def __init__(self, args):
        self._param={}
        #default values
        self._param['path_to_EDeN']="EDeN"
        self._param['model_file_path']="model"
        self._param['radius']=2
        self._param['distance']=5
        self._param['output_dir']=tempfile.mkdtemp() 
        self._param['kernel_type']="STRING"
        self._param['file_type']="STRINGSEQ"
        self._param['cluster_type']="DENSE_CONNECTED_CENTERS"
        self._param['sample_size']=1000
        self._param['num_nearest_neighbors']=10
        self._param['neighborhood_intersection_size']=int(self._param['num_nearest_neighbors']/2)
        self._param['fraction_center_scan']=1.0
        #update 
        self._param.update(args)
    
    @property
    def param(self):
        return self._param
    
    def Train(self):
        assert self._param.has_key('dat_file_path')
        assert self._param.has_key('target_file_path')
        assert self._param.has_key('model_file_path')
        
        cmd = "%(path_to_EDeN)s -a TRAIN -i %(dat_file_path)s -t %(target_file_path)s --kernel_type %(kernel_type)s --file_type %(file_type)s --radius %(radius)s --distance %(distance)s -y %(output_dir)s -m %(model_file_path)s"
        cmd = cmd % self._param

        log.info( "Executing call: %s" % cmd )
        subprocess.call( shlex.split(cmd) )

    def TestPart(self):
        assert self._param.has_key('dat_file_path')
        assert self._param.has_key('model_file_path')
       
        cmd = "%(path_to_EDeN)s -a TEST_PART -i %(dat_file_path)s --kernel_type %(kernel_type)s --file_type %(file_type)s --radius %(radius)s --distance %(distance)s -y %(output_dir)s -m %(output_dir)s/%(model_file_path)s"
        cmd = cmd % self._param

        log.info( "Executing call: %s" % cmd )
        subprocess.call( shlex.split(cmd) )
        
    def Test(self):
        assert self._param.has_key('dat_file_path')
        assert self._param.has_key('model_file_path')
       
        cmd = "%(path_to_EDeN)s -a TEST -i %(dat_file_path)s --kernel_type %(kernel_type)s --file_type %(file_type)s --radius %(radius)s --distance %(distance)s -y %(output_dir)s -m %(output_dir)s/%(model_file_path)s"
        cmd = cmd % self._param

        log.info( "Executing call: %s" % cmd )
        subprocess.call( shlex.split(cmd) )
    
    def Cluster(self):
        assert self._param.has_key('dat_file_path')

        cmd = "%(path_to_EDeN)s -a CLUSTER -i %(dat_file_path)s --kernel_type %(kernel_type)s --file_type %(file_type)s --radius %(radius)s --distance %(distance)s -y %(output_dir)s "
        cmd = cmd + "--cluster_type %(cluster_type)s --sample_size %(sample_size)s --num_nearest_neighbors %(num_nearest_neighbors)s --neighborhood_intersection_size %(neighborhood_intersection_size)s --fraction_center_scan %(fraction_center_scan)s"
        cmd = cmd % self._param

        log.info( "Executing call: %s" % cmd )
        subprocess.call( shlex.split(cmd) )