daob/automtmm

A program for the automatic analysis of MTMM data

automtmm's Issues

Getting LinAlg error that should not happen

Searching /home/daob/work/automtmm/tests/ess-round3/SK/IMSMETN...
Found r3imsmetnSK.LS8.
Running LISREL for r3imsmetnSK.LS8,Command is "wine Lisrel85.exe /home/daob/work/automtmm/tests/ess-round3/SK/IMSMETN/r3imsmetnSK.LS8 OUT".
LISREL terminated normally.
Calculating standardized matrices for r3imsmetnSK.LS8...
Reading matrix BE...BE is a FUll matrix.
Reading matrix AL...AL is a VEctor.
Reading matrix GA...GA is a FUll matrix.
Reading matrix PH...PH is a SYmmetric matrix.
Reading matrix PS...PS is a SYmmetric matrix.
Reading matrix KA...KA is a VEctor.
Reading matrix TX...TX is a VEctor.
Reading matrix TY...TY is a VEctor.
Reading matrix TD...TD is a DIagonal matrix.
Reading matrix TE...TE is a SYmmetric matrix.
Reading matrix LX...LX is a FUll matrix.
Reading matrix LY...LY is a FUll matrix.

Getting matrices for group 1 (igrp=0)

LinAlgError Traceback (most recent call last)

/home/daob/work/automtmm/ in ()

/home/daob/work/automtmm/walk_and_run.py in walk_and_run(top_dir, tempdir, action)
158 break
159 if solution_obtained(os.path.join(tempdir, 'OUT')):
--> 160 smats = lisfile.standardize_matrices()
161 for igrp in range(len(smats)):
162 for matname, stanmat in smats[igrp].iteritems():

/home/daob/work/automtmm/parse_lisrel.pyc in standardize_matrices(self, path)
262 C = np.matrix(np.sqrt(np.diag(np.diag(Eee))))
263
--> 264 ga_s = C.I * ga * np.sqrt(np.diag(np.diag(ph)))
265 ly_s = np.sqrt(np.diag(1/np.diag(Eyy))) * ly * C
266

/usr/lib/python2.6/dist-packages/numpy/core/defmatrix.pyc in getI(self)
513 else:
514 from numpy.dual import pinv as func
--> 515 return asmatrix(func(self))
516
517 def getA(self):

/usr/lib/python2.6/dist-packages/numpy/linalg/linalg.pyc in inv(a)
348 """
349 a, wrap = _makearray(a)
--> 350 return wrap(solve(a, identity(a.shape[0], dtype=a.dtype)))
351
352

/usr/lib/python2.6/dist-packages/numpy/linalg/linalg.pyc in solve(a, b)
247 results = lapack_routine(n_eq, n_rhs, a, n_eq, pivots, b, n_eq, 0)
248 if results['info'] > 0:
--> 249 raise LinAlgError, 'Singular matrix'
250 if one_eq:
251 return wrap(b.ravel().astype(result_t))

LinAlgError: Singular matrix

unit tests fail sometimes when the system is not clean

After walk_and_run, the following fail was obtained from unit tests:

ERROR: test_get_matrices (main.TestInputPT)

Traceback (most recent call last):
File "tests/test_parse_lisrel.py", line 156, in test_get_matrices
mats = self.test_input.get_matrices(path = 'temp')
File "/home/daob/work/automtmm/parse_lisrel.py", line 191, in get_matrices
(order[1], order[0])))
File "/usr/lib/python2.6/dist-packages/numpy/core/fromnumeric.py", line 145, in reshape
return reshape(newshape, order=order)
ValueError: total size of new array must be unchanged

subprocess support

os.system is now used where subprocess 'should' be used.