def test_run_external_command_fail_with_output(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.stderr.write("2error")\n')
f.write('sys.exit(2)\n')
f.flush()
f.close()
os.chmod(script, stat.S_IRWXU)
ecode, out, err = util.run_external_command(script + ' hi how')
self.assertEqual(err, '2error')
self.assertEqual(out, 'hihow')
self.assertEqual(ecode, 2)
finally:
shutil.rmtree(temp_dir)
def write_markers(self, markers):
"""Writes IMOD fiducial file with data from `markers` object passed in
:param markers: MarkersList object containing markers to write out
:raises UnsetFiducialFileError: If fiducial file set via constructor
is None
:raises UnsetMarkersListError if markers passed into this method is
None
:raises Exception: If invocation of point2model binary has non-zero
exit code
"""
if self._fiducialfile is None:
raise UnsetFiducialFileError('Fiducial File is set to None')
if markers is None:
raise UnsetMarkersListError('markers cannot be None')
try:
temp_dir = tempfile.mkdtemp()
tmpfile = os.path.join(temp_dir, 'out.txt')
markers.write_markers_to_file(tmpfile)
cmd = (self._binary + ' -circle 6 ' + tmpfile + ' ' +
self._fiducialfile)
(ecode, out, err) = util.run_external_command(cmd)
if ecode != 0:
raise Exception('Non zero exit code when running : ' + cmd +
' : ' + err)
finally:
shutil.rmtree(temp_dir)
def get_markers(self):
"""Gets markers from IMOD fiducial file
"""
markers = MarkersList()
if self._fiducialfile is None:
logger.warning('Fiducial file is set to None')
return markers
if not os.path.isfile(self._fiducialfile):
logger.warning('Fiducial file path does not point to file')
return markers
try:
temp_dir = tempfile.mkdtemp()
outfile = os.path.join(temp_dir, 'temp.txt')
cmd = (self._binary + ' -float -contour ' + self._fiducialfile +
' ' + outfile)
(ecode, out, err) = util.run_external_command(cmd)
if ecode != 0:
raise Exception('Non zero exit code when running : ' + cmd +
' : ' + err)
fac = MarkersFrom3DMarkersFileFactory(outfile)
return fac.get_markerslist()
finally:
shutil.rmtree(temp_dir)
def _run_rotatevol(self, rotation):
"""Rotates mrc volume
"""
markermrc = os.path.join(self._get_marker_dir(), self._markermrc)
tmp_mrc = os.path.join(self._get_marker_dir(), "tmp.mrc")
cmd = "rotatevol -angles " + str(rotation) + ",0,0 " + markermrc + " " + tmp_mrc
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run rotatevol : " + err)
shutil.move(tmp_mrc, markermrc)
def test_run_external_command_cmd_does_not_exist(self):
temp_dir = tempfile.mkdtemp()
try:
noexist = os.path.join(temp_dir, 'noexist')
ecode, out, err = util.run_external_command(noexist)
self.assertEqual(ecode, 255)
self.assertEqual(out, '')
self.assertEqual(err, 'Caught exception trying run command: '
'[Errno 2] No such file or directory')
finally:
shutil.rmtree(temp_dir)
def _get_mrc_marker_image_dimensions(self):
"""Gets dimensions of marker mrc file
:returns tuple: x, y, z
"""
markermrc = os.path.join(self._get_marker_dir(), self._markermrc)
cmd = "header -s " + markermrc
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run header -s : " + err)
list = re.split("\s+", out)
if len(list) != 5:
raise Exception("Invalid output from header : " + out)
return list[1], list[2], list[3]
def _run_point2model(self):
"""runs point2model for fid file
"""
two_d_fid = os.path.join(self._workdir, TiltSeriesCreator.TWO_D_MARKERS_ALL_FID)
cmd = (
"point2model -circle 6 "
+ os.path.join(self._get_tracking_dir(), TiltSeriesCreator.TWO_D_MARKERS_ALL_TXT)
+ " "
+ two_d_fid
)
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run point2model : " + err)
def _run_point2model_common(self):
"""runs point2model for fid file
"""
common_fid = os.path.join(
self._workdir, self._mrcname + TiltSeriesCreator.PROJECTION_CLIP + TiltSeriesCreator.FID_EXT
)
cmd = (
"point2model -circle 6 "
+ os.path.join(self._get_tracking_dir(), TiltSeriesCreator.TWO_D_MARKERS_COMMON_TXT)
+ " "
+ common_fid
)
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run point2model : " + err)
def _run_clip_projection_mrc(self):
"""Runs clip resize to get a clipped mrc file
"""
(x, y, z) = self._get_mrc_marker_image_dimensions()
cmd = (
"clip resize -ox "
+ str(int(int(x) / 3))
+ " -oy "
+ str(int(int(y) / 3))
+ " "
+ os.path.join(self._workdir, self._projectionmrc)
+ " "
+ os.path.join(self._workdir, self._projectionclipmrc)
)
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run clip : " + err)
def _run_rotate_3dmarkers(self, rotation):
""" Rotates 3Dmarkers.txt file
:param rotation:
:return:
"""
(x, y, z) = self._get_mrc_marker_image_dimensions()
three_d_markers_file = os.path.join(self._get_marker_dir(), TiltSeriesCreator.THREE_D_MARKERS_TXT)
cmd = (
"rotate_3dmarkers.py --angle "
+ str(rotation)
+ " --width "
+ str(x)
+ " --height "
+ str(y)
+ " "
+ three_d_markers_file
)
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run rotate_3dmarkers.py : " + err)
def _run_shift_fidfilemarkers_common(self):
"""Runs shift_fidfilemarkers to shift fid file for non clipped
projection
"""
common_fid = os.path.join(
self._workdir, self._mrcname + TiltSeriesCreator.PROJECTION_CLIP + TiltSeriesCreator.FID_EXT
)
(x, y, z) = self._get_mrc_marker_image_dimensions()
cmd = (
"shift_fidfilemarkers.py --xshift "
+ str(int(int(x) / 3))
+ " --yshift "
+ str(int(int(y) / 3))
+ " "
+ common_fid
+ " "
+ os.path.join(self._workdir, self._mrcname + TiltSeriesCreator.PROJECTION + TiltSeriesCreator.FID_EXT)
)
exitcode, out, err = util.run_external_command(cmd)
if exitcode != 0:
raise Exception("Unable to run shif_fidfilemarkers.py : " + err)
def test_run_external_command_command_not_set(self):
ecode, out, err = util.run_external_command(None)
self.assertEqual(ecode, 255)
self.assertEqual(out, '')
self.assertEqual(err, 'Command must be set')
