Python getEmanCommand Examples

Example #1

File: convert.py Project: josegutab/scipion

def createEmanProcess(script='e2converter.py', args=None, direc="."):
    """ Open a new Process with all EMAN environment (python...etc)
    that will server as an adaptor to use EMAN library
    """
    program = pw.join('em', 'packages', 'eman2', script)        
    cmd = getEmanCommand(program, args)
    
#    gcmd = greenStr(cmd)
    print "** Running: '%s'" % cmd
    proc = subprocess.Popen(cmd, shell=True, env=getEnviron(), 
                            stdin=subprocess.PIPE,
                            stdout=subprocess.PIPE, cwd=direc)
    
    return proc

Example #2

def createEmanProcess(script='e2converter.py', args=None, direc="."):
    """ Open a new Process with all EMAN environment (python...etc)
    that will server as an adaptor to use EMAN library
    """
    program = pw.join('em', 'packages', 'eman2', script)        
    cmd = getEmanCommand(program, args)
    
#    gcmd = greenStr(cmd)
    print "** Running: '%s'" % cmd
    proc = subprocess.Popen(cmd, shell=True, env=getEnviron(), 
                            stdin=subprocess.PIPE,
                            stdout=subprocess.PIPE, cwd=direc)
    
    return proc

Example #3

File: test_workflow_existing.py Project: coocoky/scipion

    def a_testEmanConvert(self):
        project = self.loadProject("TestXmippWorkflow")

        particleList = project.mapper.selectByClass('SetOfParticles')
        
        eman2.loadEnvironment()
        
        program = pw.join('em', 'packages', 'eman2', 'e2converter.py')
        
        cmd = eman2.getEmanCommand(program, 'myimage.hdf')
        
        gcmd = greenStr(cmd)
        print "** Running: '%s'" % gcmd
        proc = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE)
        
        p = particleList[0]
        for i, img in enumerate(p):
            loc = img.getLocation()
            index = loc.getIndex()
            fn = loc.getFileName()
            print >> proc.stdin, index, fn
        p.wait()

Example #4

File: test_workflow_existing.py Project: yaizar/scipion-docker

    def a_testEmanConvert(self):
        project = self.loadProject("TestXmippWorkflow")

        particleList = project.mapper.selectByClass('SetOfParticles')
        
        eman2.loadEnvironment()
        
        program = pw.join('em', 'packages', 'eman2', 'e2converter.py')
        
        cmd = eman2.getEmanCommand(program, 'myimage.hdf')
        
        gcmd = greenStr(cmd)
        print "** Running: '%s'" % gcmd
        proc = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE)
        
        p = particleList[0]
        for i, img in enumerate(p):
            loc = img.getLocation()
            index = loc.getIndex()
            fn = loc.getFileName()
            print >> proc.stdin, index, fn
        p.wait()