def _run_project_all(self):
"""Runs project_all
"""
projectiondir = self._get_projection_dir()
if not os.path.isdir(projectiondir):
os.makedirs(projectiondir)
cmd = (
os.path.join(self._etspecbin, "project_all")
+ " "
+ os.path.join(self._get_marker_dir(), self._markermrc)
+ " "
+ os.path.join(self._workdir, self._projectionmrc)
+ " "
+ str(self._begintilt)
+ " "
+ str(self._tiltshift)
+ " "
+ str(self._endtilt)
+ " "
+ str(self._shrinkage)
+ " "
+ str(self._projmaxangle)
+ " 0 0 0 0"
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, self._cores)
if exitcode != 0:
raise Exception("Unable to run project_all : " + err)
def _run_volume_marker_position_all(self):
"""Runs volume_marker_position_all
"""
trackingdir = self._get_tracking_dir()
if not os.path.isdir(trackingdir):
os.makedirs(trackingdir)
cmd = (
os.path.join(self._etspecbin, "volume_marker_position_all")
+ " "
+ os.path.join(self._get_marker_dir(), self._markermrc)
+ " "
+ os.path.join(self._get_marker_dir(), TiltSeriesCreator.THREE_D_MARKERS_TXT)
+ " "
+ os.path.join(self._get_projection_dir(), TiltSeriesCreator.OFFSET_ALL_TXT)
+ " "
+ str(self._nummarkers)
+ " "
+ str(self._begintilt)
+ " "
+ str(self._tiltshift)
+ " "
+ str(self._endtilt)
+ " "
+ str(self._shrinkage)
+ " "
+ str(self._projmaxangle)
+ " 0 0 0 0"
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, 1)
if exitcode != 0:
raise Exception("Unable to run volume_marker_position_all : " + err)
def test_run_mpiexec_command_fail_with_cores_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
script = os.path.join(temp_dir, 'yo.py')
# create a small python script that outputs args passed
# in to standard out, writes error to standard error
# and exits with 0 exit code
f = open(script, 'w')
f.write('#! /usr/bin/env python\n\n')
f.write('import sys\n')
f.write('sys.stdout.write(sys.argv[1])\n')
f.write('sys.stdout.write(sys.argv[2])\n')
f.write('sys.stdout.write(sys.argv[3])\n')
f.write('sys.stderr.write("error")\n')
f.write('sys.exit(1)\n')
f.flush()
f.close()
os.chmod(script, stat.S_IRWXU)
ecode, out, err = util.run_mpiexec_command('foo', script, None)
self.assertEqual(err, 'error')
self.assertEqual(out, '-np1foo')
self.assertEqual(ecode, 1)
finally:
shutil.rmtree(temp_dir)
def _run_extend_mean(self):
"""Runs exteand_mean command
"""
cmd = (
os.path.join(self._etspecbin, "extend_mean")
+ " "
+ os.path.join(self._workdir, self._unimrc)
+ " "
+ os.path.join(self._workdir, self._extmeanmrc)
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, self._cores)
if exitcode != 0:
raise Exception("Unable to run extend_mean : " + err)
def _run_all_255(self):
"""Runs all_255 command
"""
cmd = (
os.path.join(self._etspecbin, "all_255")
+ " "
+ self._inputmrc
+ " "
+ os.path.join(self._workdir, self._unimrc)
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, self._cores)
if exitcode != 0:
raise Exception("Unable to run all_255 : " + err)
def _run_raw_tilt(self):
"""Runs exteand_mean command
"""
cmd = (
os.path.join(self._etspecbin, "rawtlt")
+ " "
+ str(self._begintilt)
+ " "
+ str(self._tiltshift)
+ " "
+ str(self._endtilt)
+ " "
+ os.path.join(self._workdir, self._rawtlt)
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, 1)
if exitcode != 0:
raise Exception("Unable to run rawtlt : " + err)
def _run_warpz(self):
"""Runs exteand_mean command
"""
warpzdir = self._get_warpz_dir()
if not os.path.isdir(warpzdir):
os.makedirs(warpzdir)
cmd = (
os.path.join(self._etspecbin, "warpZ_inter_del")
+ " "
+ os.path.join(self._workdir, self._extmeanmrc)
+ " "
+ os.path.join(self._workdir, self._extmeanmrc)
+ " "
+ os.path.join(warpzdir, self._warpz)
+ " "
+ str(self._get_number_of_tilts())
+ " 0 0 0 0"
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, self._cores)
if exitcode != 0:
raise Exception("Unable to run warpZ_inter_del : " + err)
def _run_volume_marker(self):
"""Runs exteand_mean command
"""
markerdir = self._get_marker_dir()
if not os.path.isdir(markerdir):
os.makedirs(markerdir)
warpzdir = self._get_warpz_dir()
cmd = (
os.path.join(self._etspecbin, "volume_marker")
+ " "
+ os.path.join(self._workdir, self._extmeanmrc)
+ " "
+ os.path.join(warpzdir, self._warpz)
+ " "
+ os.path.join(markerdir, self._markermrc)
+ " "
+ str(self._nummarkers)
+ " "
+ str(self._bottommarkersize)
+ " "
+ str(self._topmarkersize)
+ " "
+ str(self._markernoise)
+ " "
+ str(self._get_number_of_tilts())
+ " 0 0 0 0 0 "
+ str(self._markera)
+ " "
+ str(self._aparam)
)
exitcode, out, err = util.run_mpiexec_command(cmd, self._mpiexec, self._cores)
if exitcode != 0:
raise Exception("Unable to run rawtlt : " + err)
def test_run_mpiexec_command_with_mpiexec_not_set(self):
ecode, out, err = util.run_mpiexec_command('foo', None, None)
self.assertEqual(ecode, 255)
self.assertEqual(out, '')
self.assertEqual(err, 'mpiexec must be set')
