Example #1
0
    def testNeuroMorpho(self):



        for f in self.get_neuroMorphFilenames():

            m = MorphologyArray.fromSWC(open(f))

            print 'Loaded', f, "(%d Vertices)" % len(m)

            swcOut = m.toSWC()

            dtype= {'names':   ('id', 'type', 'x', 'y', 'z', 'r', 'pid'), 'formats': ('int32', 'int32', 'f4', 'f4', 'f4', 'f4', 'int32') }
            swcDataSrc = np.loadtxt(open(f), dtype=dtype)
            swcDataOut = np.loadtxt(StringIO(swcOut), dtype=dtype)

            eps = 0.01
            assert (swcDataSrc['id'] == swcDataOut['id']).all()
            assert (swcDataSrc['pid'] == swcDataOut['pid']).all()
            maxX = np.max(np.fabs(swcDataSrc['x'] - swcDataOut['x']))
            maxY = np.max(np.fabs(swcDataSrc['y'] - swcDataOut['y']))
            maxZ = np.max(np.fabs(swcDataSrc['z'] - swcDataOut['z']))
            maxR = np.max(np.fabs(swcDataSrc['r'] - swcDataOut['r']))
            maxEPS = np.max((maxX, maxY, maxZ, maxR))
            assert maxEPS < eps
            print ' -- Max EPS: %f' % maxEPS
Example #2
0
    def test1(self):
        swcSrc = """
        1 0 1.0 2.0 3.0 4.0 -1
        2 0 5.0 6.0 7.0 8.0 1
        """

        swcOut = MorphologyArray.fromSWC(StringIO(swcSrc)).to_tree().toSWCStr()

        print "*", StrUtils.strip_comments_and_blank_lines(swcSrc), "*"
        print "*", StrUtils.strip_comments_and_blank_lines(swcOut), "*"
        assert StrUtils.strip_comments_and_blank_lines(swcSrc) == StrUtils.strip_comments_and_blank_lines(swcOut)


        m=MorphologyArray.fromSWC(StringIO(swcSrc))
        s = m.toSWC()
        print s