def testLoadPDB(self):
""" Check that we can load a pdb and convert it to a dict. """
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check exception on corrupt file.
# does not raise due to highly tolerant default acceptance levels in Bio.PDB.
#self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("2nip_corrupt.pdb" ) )
# Check exception on wrong input type.
self.assertRaises( IOError, IOUtilities.loadPDB, [1,2] )
# Check exception on wrong file type.
self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("sample.h5") )
def backengine(self):
""" This method drives the backengine CrystFEL.pattern_sim."""
# pattern_sim backengine does not support MPI.
return self._run()
# collect MPI arguments
if self.parameters.forced_mpi_command == "":
np = self.computeNTasks()
mpicommand = ParallelUtilities.prepareMPICommandArguments(np)
else:
mpicommand = self.parameters.forced_mpi_command
# Dump to a temporary file.
fname = IOUtilities.getTmpFileName()
self.dumpToFile(fname)
mpicommand += " ".join([" ", sys.executable, __file__, fname])
args = shlex.split(mpicommand)
if 'SIMEX_VERBOSE' in os.environ and os.environ[
'SIMEX_VERBOSE'] == 'MPI':
print("MPI command: " + mpicommand)
try:
proc = subprocess.Popen(args, universal_newlines=True)
proc.wait()
except:
raise
finally:
os.remove(fname)
return proc.returncode
def testLoadPDB(self):
""" Check that we can load a pdb and convert it to a dict. """
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check exception on wrong input type.
self.assertRaises( IOError, IOUtilities.loadPDB, [1,2] )
# Check exception on wrong file type.
self.assertRaises( IOError, IOUtilities.loadPDB, generateTestFilePath("sample.h5") )
def backengine(self):
""" Starts WPG simulations in parallel in a subprocess """
fname = IOUtilities.getTmpFileName()
self.dumpToFile(fname)
forcedMPIcommand = self.parameters.forced_mpi_command
if forcedMPIcommand == "":
(np, ncores) = self.computeNTasks()
mpicommand = ParallelUtilities.prepareMPICommandArguments(
np, ncores)
else:
mpicommand = forcedMPIcommand
if 'SIMEX_VERBOSE' in os.environ:
if 'MPI' in os.environ['SIMEX_VERBOSE']:
print(("WavePropagator backengine mpicommand: " + mpicommand))
if 'PYTHON' in os.environ['SIMEX_VERBOSE']:
import platform
print("Running python %s." % (platform.python_version()))
mpicommand += " python " + __file__ + " " + fname
args = shlex.split(mpicommand)
proc = subprocess.Popen(args, universal_newlines=True)
proc.wait()
os.remove(fname)
return proc.returncode
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
raise ValueError( "A sample must be defined.")
if val.split(".")[-1] == "pdb":
print("Checking presence of %s. Will query from PDB if not found in $PWD." % (val))
self.__sample = IOUtilities.checkAndGetPDB(val)
print("Sample path is set to %s." % (self.__sample))
def testGenesisDFLToWPGWavefront(self):
""" Check the conversion from genesis dfl to wpg readable hdf5. """
genesis_out_file = generateTestFilePath("genesis/lcls/lcls.out")
genesis_dfl_file = generateTestFilePath("genesis/lcls/lcls.out.dfl")
wf = IOUtilities.genesis_dfl_to_wavefront(genesis_out_file, genesis_dfl_file)
self.assertIsInstance(wf, Wavefront)
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
self.__sample = None
return
if val.split(".")[-1] == "pdb":
self.__sample = IOUtilities.checkAndGetPDB(val)
return
raise IOError("Samples must be in pdb format.")
def testQueryPDBTwice(self):
""" Check that we can do two subsequent queries (fails if urllib.urlcleanup is not called.) """
# Setup path to pdb file.
pdb_path = '5loy.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
# Remove it.
os.remove(pdb_path)
# Query again.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
def testQueryPDB(self):
""" Check that we can query a non-existing pdb from pdb.org and convert it to a dict. """
# Setup path to pdb file.
pdb_path = '5UDC.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
pdb_path = IOUtilities.checkAndGetPDB(pdb_path)
# Check it's there.
self.assertTrue( os.path.isfile( pdb_path ) )
def backengine(self):
""" Starts EMC simulations in parallel in a subprocess """
# Set paths.
self._setupPaths()
fname = IOUtilities.getTmpFileName()
self.dumpToFile(fname)
# collect MPI arguments
if self.parameters.forced_mpi_command == "":
np = self.computeNTasks()
#mpicommand=ParallelUtilities.prepareMPICommandArguments(np)
mpicommand = ""
else:
mpicommand = self.parameters.forced_mpi_command
# collect program arguments
command_sequence = [
'python',
__file__,
fname,
]
# put MPI and program arguments together
args = shlex.split(mpicommand) + command_sequence
print(' '.join(args))
if 'SIMEX_VERBOSE' in os.environ:
if 'MPI' in os.environ['SIMEX_VERBOSE']:
print(("EMCOrientation backengine mpicommand: " + mpicommand))
print(' '.join(args))
if 'PYTHON' in os.environ['SIMEX_VERBOSE']:
import platform
print("Running python version %s." %
(platform.python_version()))
# Run the backengine command.
proc = subprocess.Popen(args)
proc.wait()
os.remove(fname)
# Return the return code from the backengine.
return proc.returncode
def testLoadXYZ(self):
""" Check that we can load a xyz file and convert it to a dict. """
# Setup path to xyz file.
xyz_path = generateTestFilePath("Fe2O3_poly_test.xyz")
# Attempt to load it.
return_dict = IOUtilities.loadXYZ(xyz_path)
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (100,) )
self.assertEqual( return_dict['r'].shape, (100,3) )
def testPdbToS2ESampleDict(self):
""" Check the utility that converts a pdb file to an s2e sample dict.
"""
# Setup path to pdb file.
pdb_path = generateTestFilePath("2nip.pdb")
# Attempt to load it.
return_dict = IOUtilities._pdbToS2ESampleDict(pdb_path)
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
def _backengineWithPdb(self):
""" """
"""
Run the diffraction simulation if the sample is a pdb.
Codes is based on pysingfel/tests/test_particle.test_calFromPDB
"""
# Dump self to file.
fname = IOUtilities.getTmpFileName()
self.dumpToFile(fname)
# Setup the mpi call.
forcedMPIcommand = self.parameters.forced_mpi_command
if forcedMPIcommand == "" or forcedMPIcommand is None:
(np, ncores) = self.computeNTasks()
mpicommand = ParallelUtilities.prepareMPICommandArguments(
np, ncores)
else:
mpicommand = forcedMPIcommand
mpicommand += " ".join(("", sys.executable, __file__, fname))
if 'SIMEX_VERBOSE' in os.environ:
if 'MPI' in os.environ['SIMEX_VERBOSE']:
print(("SingFELPhotonDiffractor backengine mpicommand: " +
mpicommand))
# Launch the system command.
args = shlex.split(mpicommand)
with subprocess.Popen(args, universal_newlines=True) as proc:
out, err = proc.communicate()
# Remove the dumped class.
os.remove(fname)
return proc.returncode
def notestQueryPDB(self):
""" Check that we can query a non-existing pdb from pdb.org and convert it to a dict. """
# Setup path to pdb file.
pdb_path = '2nip.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
# Check exception on wrong input type.
self.assertRaises( IOError, IOUtilities.loadPDB, 'xyz.pdb' )
def testQueryPDBDirectory(self):
""" Check that if the pdb does not exist in the local database, it is queried from pdb.org, save in a dir, and convert it to a dict. """
# Setup path to pdb file.
pdb_path = 'pdb/2nip.pdb'
self.__files_to_remove.append(pdb_path)
self.__paths_to_remove.append('obsolete')
self.__paths_to_remove.append('pdb')
os.mkdir('pdb')
# Attempt to load it.
return_dict = IOUtilities.loadPDB(pdb_path)
# Check items on dict.
self.assertIsInstance( return_dict['Z'], numpy.ndarray )
self.assertIsInstance( return_dict['r'], numpy.ndarray )
self.assertIsInstance( return_dict['selZ'], dict )
self.assertIsInstance( return_dict['N'], int )
self.assertEqual( return_dict['Z'].shape, (4728,) )
self.assertEqual( return_dict['r'].shape, (4728,3) )
# Check that return type is a dict.
self.assertIsInstance( return_dict, dict )
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
raise ValueError( "A sample must be defined.")
if val.split(".")[-1] == "pdb":
self.__sample = IOUtilities.checkAndGetPDB(val)
def backengine(self):
""" This method drives the backengine singFEL."""
uniform_rotation = self.parameters.uniform_rotation
calculate_Compton = int(self.parameters.calculate_Compton)
slice_interval = self.parameters.slice_interval
number_of_slices = self.parameters.number_of_slices
pmi_start_ID = self.parameters.pmi_start_ID
pmi_stop_ID = self.parameters.pmi_stop_ID
number_of_diffraction_patterns = self.parameters.number_of_diffraction_patterns
if not os.path.isdir(self.output_path):
os.mkdir(self.output_path)
self.__output_dir = self.output_path
# If the sample is passed as a pdb, branch out to separate backengine implementation.
if self.input_path.split(".")[-1].lower() == 'pdb':
if not os.path.isfile(self.input_path):
# Attempt to query from pdb.
self.input_path = IOUtilities.checkAndGetPDB(self.input_path)
return self._backengineWithPdb()
# Ok, not a pdb, proceed.
# Serialize the geometry file.
beam_geometry_file = "tmp.geom"
self.parameters.detector_geometry.serialize(beam_geometry_file)
# Setup directory to pmi output.
# Backengine expects a directory name, so have to check if
# input_path is dir or file and handle accordingly.
if os.path.isdir(self.input_path):
input_dir = self.input_path
elif os.path.isfile(self.input_path):
input_dir = os.path.dirname(self.input_path)
config_file = '/dev/null'
# collect MPI arguments
if self.parameters.forced_mpi_command == "":
np, ncores = self.computeNTasks()
mpicommand = ParallelUtilities.prepareMPICommandArguments(np,1)
else:
mpicommand = self.parameters.forced_mpi_command
# collect program arguments
command_sequence = ['radiationDamageMPI',
'--inputDir', str(input_dir),
'--outputDir', str(self.__output_dir),
'--geomFile', str(beam_geometry_file),
'--configFile', str(config_file),
'--uniformRotation', str(uniform_rotation),
'--calculateCompton', str(calculate_Compton),
'--sliceInterval', str(slice_interval),
'--numSlices', str(number_of_slices),
'--pmiStartID', str(pmi_start_ID),
'--pmiEndID', str(pmi_stop_ID),
'--numDP', str(number_of_diffraction_patterns),
]
if self.parameters.beam_parameters is not None:
beam_parameter_file = "tmp.beam"
self.parameters.beam_parameters.serialize(beam_parameter_file)
command_sequence.append('--beamFile')
command_sequence.append(str(beam_parameter_file))
# put MPI and program arguments together
args = shlex.split(mpicommand) + command_sequence
if 'SIMEX_VERBOSE' in os.environ:
print(("SingFELPhotonDiffractor backengine command: "
+ " ".join(args)),flush=True)
# Run the backengine command.
proc = subprocess.Popen(args)
proc.wait()
# Return the return code from the backengine.
return proc.returncode
def backengine(self):
""" This method drives the backengine code."""
status = 0
input_files = []
if os.path.isfile(self.input_path):
input_files = [self.input_path]
elif os.path.isdir(self.input_path):
input_files = [ os.path.join( self.input_path, f) for f in os.listdir( self.input_path ) if f.split('.')[-1] == 'h5' and f.split('.')[-2] != 'opmd' ]
input_files.sort()
else:
raise IOError("Input file %s does not exist or cannot be read." % (self.input_path) )
# Create output directory if not existing yet.
if not os.path.isdir( self.output_path ):
os.mkdir( self.output_path )
elif os.path.isfile( self.output_path ):
raise IOError( "Output file %s already exists, cowardly refusing to overwrite." % (self.output_path) )
# Generate formatted output files (i.e. attach history to output file).
for i,input_file in enumerate(input_files):
tail = input_file.split( 'prop' )[-1]
output_file = os.path.join( self.output_path , 'pmi_out_%07d.h5' % (i+1) )
pmi_script.f_h5_out2in( input_file, output_file)
# Get the backengine calculator.
pmi_demo = PMIDemo()
# Transfer some parameters.
pmi_demo.g_s2e['prj'] = ''
pmi_demo.g_s2e['id'] = tail.split('_')[-1].split('.')[0]
pmi_demo.g_s2e['prop_out'] = input_file
pmi_demo.g_s2e['setup'] = dict()
pmi_demo.g_s2e['sys'] = dict()
pmi_demo.g_s2e['setup']['num_digits'] = 7
if 'number_of_steps' in self.parameters.keys():
pmi_demo.g_s2e['steps'] = self.parameters['number_of_steps']
else:
pmi_demo.g_s2e['steps'] = 100
pmi_demo.g_s2e['maxZ'] = 100
pmi_demo.g_s2e['setup']['pmi_out'] = output_file
# Setup the database.
pmi_demo.f_dbase_setup()
# Go through the pmi workflow.
pmi_demo.f_init_random()
pmi_demo.f_save_info()
pmi_demo.f_load_pulse( pmi_demo.g_s2e['prop_out'] )
# Check if sample is a h5 file. Horrible hack.
try:
h5 = h5py.File(self.__sample_path)
h5.close()
pmi_demo.f_load_sample(self.__sample_path)
except:
# Assume it's a pdb file. Will raise if not.
atoms_dict = IOUtilities.loadPDB(self.__sample_path)
pmi_demo.g_s2e['sample'] = atoms_dict
pmi_demo.f_rotate_sample()
pmi_demo.f_system_setup()
# Perform the trajectories for this pulse and orientation.
for traj in range( self.parameters['number_of_trajectories'] ):
pmi_demo.f_time_evolution()
return status