def runGautomatchStep(self, micName, refStack, args):
# We convert the input micrograph on demand if not in .mrc
runGautomatch(micName,
refStack,
self.getMicrographsDir(),
args,
env=self._getEnviron())
def _pickMicrograph(self, mic, args):
micName = mic.getFileName()
if self.inputReferences.get():
refStack = self._getExtraPath('references.mrcs')
else:
refStack = None
# We convert the input micrograph on demand if not in .mrc
runGautomatch(micName,
refStack,
self.getMicrographsDir(),
args,
env=self._getEnviron())
def _pickMicrographList(self, micList, args):
""" Pick several micrographs at once, probably a bit more efficient."""
micFnList = []
for mic in micList:
micFn = mic.getFileName()
micFnList.append(micFn)
# The coordinates conversion is done for each micrograph
# and not in convertInputStep, this is needed for streaming
badCoords = self.inputBadCoords.get()
if self.exclusive and badCoords:
fnCoords = os.path.join(self.getMicrographsDir(), '%s_rubbish.star'
% pwutils.removeBaseExt(micFn))
writeMicCoords(mic, badCoords.iterCoordinates(mic), fnCoords)
# We convert the input micrograph on demand if not in .mrc
runGautomatch(micFnList,
self._getReferencesFn(),
self.getMicrographsDir(),
args,
env=self._getEnviron(),
runJob=self.runJob)
def _pickMicrographList(self, micList, args):
""" Pick several micrographs at once, probably a bit more efficient."""
micFnList = []
for mic in micList:
micFn = mic.getFileName()
micFnList.append(micFn)
# The coordinates conversion is done for each micrograph
# and not in convertInputStep, this is needed for streaming
badCoords = self.inputBadCoords.get()
if self.exclusive and badCoords:
fnCoords = os.path.join(
self.getMicrographsDir(),
'%s_rubbish.star' % pwutils.removeBaseExt(micFn))
writeMicCoords(mic, badCoords.iterCoordinates(mic), fnCoords)
# We convert the input micrograph on demand if not in .mrc
runGautomatch(micFnList,
self._getReferencesFn(),
self.getMicrographsDir(),
args,
env=self._getEnviron(),
runJob=self.runJob)
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
import sys
from convert import runGautomatch
if __name__ == '__main__':
micName = sys.argv[1]
refStack = sys.argv[2]
workDir = sys.argv[3]
args = " ".join(sys.argv[4:])
runGautomatch([micName], refStack, workDir, args)
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
import sys
from convert import runGautomatch
if __name__ == '__main__':
micName = sys.argv[1]
refStack = sys.argv[2]
workDir = sys.argv[3]
args = " ".join(sys.argv[4:])
runGautomatch([micName], refStack, workDir, args)