def initialize_experiment(cfg):
"""takes a yml configuration file as input"""
# make experiment
ws = expt.Experiment()
cwd = cfg.working_dir
materials_fname = cfg.material.definitions
material_name = cfg.material.active
detector_fname = cfg.instrument.detector.parameters_old
# load materials
ws.loadMaterialList(os.path.join(cwd, materials_fname))
ws.activeMaterial = material_name
logger.info("setting active material to '%s'", material_name)
pd = ws.activeMaterial.planeData
# detector data
try:
reader = ReadGE(cfg.image_series.omegaseries)
except IOError:
logger.info("raw data not found, skipping reader init")
reader = None
try:
ws.loadDetector(os.path.join(cwd, detector_fname))
detector = ws.detector
except IOError:
logger.info(
"old detector par file not found, skipping; \nalthough you may need this for find-orientations"
)
detector = None
return pd, reader, detector
def initialize_experiment(cfg):
"""takes a yml configuration file as input"""
# make experiment
ws = expt.Experiment()
cwd = cfg.working_dir
materials_fname = cfg.material.definitions
material_name = cfg.material.active
detector_fname = cfg.instrument.detector.parameters_old
# load materials
ws.loadMaterialList(os.path.join(cwd, materials_fname))
ws.activeMaterial = material_name
logger.info("setting active material to '%s'", material_name)
pd = ws.activeMaterial.planeData
image_start = cfg.image_series.images.start
dark = cfg.image_series.dark
flip = cfg.image_series.flip
# detector data
try:
reader = ReadGE(
[(f, image_start) for f in cfg.image_series.files],
np.radians(cfg.image_series.omega.start),
np.radians(cfg.image_series.omega.step),
subtractDark=dark is not None, # TODO: get rid of this
dark=dark,
doFlip=flip is not None,
flipArg=flip, # TODO: flip=flip
)
except IOError:
logger.info("raw data not found, skipping reader init")
reader = None
try:
ws.loadDetector(os.path.join(cwd, detector_fname))
detector = ws.detector
except IOError:
logger.info(
"old detector par file not found, skipping; \nalthough you may need this for find-orientations"
)
detector = None
return pd, reader, detector
def initialize_experiment(cfg_file):
"""
"""
parser = SafeConfigParser()
parser.read(cfg_file)
hexrd_root = parser.get('base', 'hexrd_root')
# make experiment
ws = expt.Experiment(cfgFile=os.path.join(hexrd_root,
"hexrd/data/materials.cfg"),
matFile=os.path.join(hexrd_root,
"hexrd/data/all_materials.cfg"))
working_dir = parser.get('base', 'working_dir')
materials_fname = parser.get('material', 'materials_fname')
material_name = parser.get('material', 'material_name')
detector_fname = parser.get('detector', 'parfile_name')
# MATERIALS
ws.loadMaterialList(os.path.join(working_dir, materials_fname))
ws.activeMaterial = material_name
print "setting active material to '%s'" % (material_name)
pd = ws.activeMaterial.planeData
image_dir = parser.get('reader', 'image_dir')
# number of files ASSUMING SEQUENTIAL SCAN NUMBERS
file_start = parser.getint('reader', 'file_start')
file_stop = parser.getint('reader', 'file_stop')
file_suffix = parser.get('reader', 'file_suffix')
nfiles = file_stop - file_start + 1
zpad_str = '%0' + parser.get('reader', 'file_zpad') + 'd' # int
fileInfo = []
for i in [file_start + i for i in range(nfiles)]:
if file_suffix == '':
image_filename = parser.get('reader',
'file_root') + '_' + zpad_str % (i)
else:
image_filename = parser.get(
'reader',
'file_root') + '_' + zpad_str % (i) + '.' + file_suffix
fileInfo.append(
(os.path.join(image_dir,
image_filename), parser.getint('reader', 'nempty')))
ome_start = parser.getfloat('reader', 'ome_start') * d2r
ome_delta = parser.getfloat('reader', 'ome_delta') * d2r
darkName = parser.get('reader', 'dark')
if darkName.strip() == '':
dark = None
subtractDark = False
else:
# dark = os.path.join(image_dir, darkName)
dark = darkName
subtractDark = True
doFlip = parser.getboolean('reader', 'doFlip')
flipArg = parser.get('reader', 'flipArg')
# make frame reader
reader = ReadGE(fileInfo,
ome_start,
ome_delta,
subtractDark=subtractDark,
dark=dark,
doFlip=doFlip,
flipArg=flipArg)
# DETECTOR
ws.loadDetector(os.path.join(working_dir, detector_fname))
return pd, reader, ws.detector
def get_diffraction_angles(self):
cfg = self.cfg
logger = self.logger
detector = self.detector
# Number of cores for multiprocessing
num_cores = cfg.multiprocessing
# Initialize a new heXRD experiment
ws = expt.Experiment()
cwd = cfg.working_dir
materials_fname = cfg.material.definitions
material_name = cfg.material.active
detector_fname = cfg.instrument.detector.parameters_old
# load materials
ws.loadMaterialList(os.path.join(cwd, materials_fname))
mat_name_list = ws.matNames
# Create an array of all the essential parameters to be
# sent to parallel diffraction angle calculation routine
fwd_model_input = []
for xyz_i, mat_name_i, quat_i, defgrad_i in zip(
self.ms_grid, self.ms_material_ids, self.ms_quaternions,
self.ms_lat_defgrads):
# Set chi tilt
if detector.chiTilt is not None:
chi = detector.chiTilt
else:
chi = 0.0
# Obtain all symmetric hkls for the material
ws.activeMaterial = mat_name_i.strip() #material_name
hkls = ws.activeMaterial.planeData.getSymHKLs()
hkls = np.transpose(np.hstack(hkls))
# Rotational matrix from the orientation/quaternion
rmat_c = rot.rotMatOfQuat(quat_i)
# bmat
bmat = ws.activeMaterial.planeData.latVecOps['B']
wavelength = ws.activeMaterial.planeData.wavelength
# Create a dictionary of inputs to be sent to the MP worker
fwd_model_input.append({
'chi': chi,
'hkls': hkls,
'rmat_c': rmat_c,
'bmat': bmat,
'wavelength': wavelength,
'defgrad_i': defgrad_i
})
# Now we have the data, run eta, twoth, omega calculations in parallel
logger.info(
"Starting virtual diffraction calculations using %i processors",
num_cores)
synth_angles_MP_output = Parallel(n_jobs=num_cores, verbose=5)(
delayed(get_diffraction_angles_MP)(fwd_model_input_i)
for fwd_model_input_i in fwd_model_input)
synth_angles = np.vstack(synth_angles_MP_output)
self.synth_angles = synth_angles
return synth_angles