def prep_output(self):
''' Assign output paths to image object (will be used by various modules
to write out files in appropriate locations) '''
# Get bases
input_base = self.info.input_base if self.info else self.init.input_base
obj_base = self.info.obj_base if self.info else self.init.obj_base
fin_base = self.info.fin_base if self.info else self.init.fin_base
log_base = self.info.log_base if self.info else self.init.log_base
viz_base = self.info.viz_base if self.info else self.init.viz_base
# Object path (may not need)
self.img_object.obj_path = util.make_image_path(
self.img_object.img_path, input_base, obj_base)
fname = util.make_filename(self.img_object.img_path, new_ext='int')
self.img_object.obj_file = os.path.join(self.img_object.obj_path,
fname)
# Final integration pickle path
self.img_object.int_path = util.make_image_path(
self.img_object.img_path, input_base, fin_base)
fname = util.make_filename(self.img_object.img_path,
prefix='int',
new_ext='pickle')
self.img_object.int_file = os.path.join(self.img_object.int_path,
fname)
# Processing log path for image
self.img_object.log_path = util.make_image_path(
self.img_object.img_path, input_base, log_base)
fname = util.make_filename(self.img_object.img_path, new_ext='log')
self.img_object.int_log = os.path.join(self.img_object.log_path, fname)
# Visualization path (may need to deprecate)
self.img_object.viz_path = util.make_image_path(
self.img_object.img_path, input_base, viz_base)
fname = util.make_filename(self.img_object.img_path,
prefix='int',
new_ext='png')
self.viz_file = os.path.join(self.img_object.viz_path, fname)
# Make paths if they don't exist already
for path in [
self.img_object.obj_path, self.img_object.int_path,
self.img_object.log_path, self.img_object.viz_path
]:
try:
os.makedirs(path)
except OSError:
pass
# Populate the 'final' dictionary
self.img_object.final['final'] = self.img_object.int_file
self.img_object.final['img'] = self.img_object.img_path
def prep_output(self):
''' Assign output paths to image object (will be used by various modules
to write out files in appropriate locations) '''
# Object path (may not need)
self.img_object.obj_path = util.make_image_path(self.img_object.img_path,
self.init.input_base,
self.init.obj_base)
fname = util.make_filename(self.img_object.img_path, new_ext='int')
self.img_object.obj_file = os.path.join(self.img_object.obj_path, fname)
# Final integration pickle path
self.img_object.int_path = util.make_image_path(self.img_object.img_path,
self.init.input_base,
self.init.fin_base)
fname = util.make_filename(self.img_object.img_path, prefix='int',
new_ext='pickle')
self.img_object.int_file = os.path.join(self.img_object.int_path, fname)
# Processing log path for image
self.img_object.log_path = util.make_image_path(self.img_object.img_path,
self.init.input_base,
self.init.log_base)
fname = util.make_filename(self.img_object.img_path, new_ext='tmp')
self.img_object.int_log = os.path.join(self.img_object.log_path, fname)
# Visualization path (may need to deprecate)
self.img_object.viz_path = util.make_image_path(self.img_object.img_path,
self.init.input_base,
self.init.viz_base)
fname = util.make_filename(self.img_object.img_path, prefix='int',
new_ext='png')
self.viz_file = os.path.join(self.img_object.viz_path, fname)
# Populate the 'final' dictionary
self.img_object.final['final'] = self.img_object.int_file
self.img_object.final['img'] = self.img_object.img_path
def rename_converted_image(self, filepath):
# Generate converted image pickle filename
rename_choice = str(
self.params.cctbx_ha14.image_conversion.rename_pickle).lower()
if rename_choice in ("keep_file_structure", "none"):
img_dir = util.make_image_path(filepath, self.input_base,
self.conv_base)
img_filename = util.make_filename(filepath, new_ext='pickle')
else:
self.input_base = self.conv_base
if rename_choice == "auto_filename":
prefix = self.init.user_id
elif rename_choice == "custom_filename":
prefix = self.params.cctbx_ha14.image_conversion.rename_pickle_prefix
else:
prefix = 'iota'
img_dir = self.conv_base
number = int(os.path.basename(self.conv_base))
img_filename = "{}_{}_{:05d}.pickle" \
"".format(prefix, number, self.img_object.img_index)
return os.path.abspath(os.path.join(img_dir, img_filename))
def prep_output(self):
''' Assign output paths to image object (will be used by various modules
to write out files in appropriate locations) '''
# Get bases
input_base = self.info.input_base if self.info else self.init.input_base
obj_base = self.info.obj_base if self.info else self.init.obj_base
fin_base = self.info.fin_base if self.info else self.init.fin_base
log_base = self.info.log_base if self.info else self.init.log_base
dials_log_base = self.info.dials_log_base if self.info else None
viz_base = self.info.viz_base if self.info else self.init.viz_base
# Set prefix (image index in multi-image files, or None otherwise)
if self.img_object.is_multi_image:
image_index = self.img_object.img_index
else:
image_index = None
# Object path (may not need)
self.img_object.obj_path = util.make_image_path(self.img_object.img_path,
input_base, obj_base)
fname = util.make_filename(prefix=image_index,
path=self.img_object.img_path,
new_ext='int')
self.img_object.obj_file = os.path.join(self.img_object.obj_path, fname)
# DIALS process filepaths
# Indexed reflections
ridx_path = util.make_filename(
prefix=image_index,
path=self.img_object.img_path,
suffix='indexed',
new_ext='refl'
)
self.img_object.ridx_path = os.path.join(self.img_object.obj_path,
ridx_path)
# Spotfinding (strong) reflections
rspf_path = util.make_filename(
prefix=image_index,
path=self.img_object.img_path,
suffix='strong',
new_ext='refl'
)
self.img_object.rspf_path = os.path.join(self.img_object.obj_path,
rspf_path)
# Refined experiments
eref_path = util.make_filename(
prefix=image_index,
path=self.img_object.img_path,
suffix='refined',
new_ext='expt'
)
self.img_object.eref_path = os.path.join(self.img_object.obj_path,
eref_path)
# Integrated experiments
eint_path = util.make_filename(
prefix=image_index,
path=self.img_object.img_path,
suffix='integrated',
new_ext='expt'
)
self.img_object.eint_path = os.path.join(self.img_object.obj_path,
eint_path)
# Integrated reflections
rint_path = util.make_filename(
prefix=image_index,
path=self.img_object.img_path,
suffix='integrated',
new_ext='refl'
)
self.img_object.rint_path = os.path.join(self.img_object.obj_path,
rint_path)
# Final integration pickle path
self.img_object.int_path = util.make_image_path(self.img_object.img_path,
input_base, fin_base)
fname = util.make_filename(path=self.img_object.img_path,
prefix='int',
suffix=image_index,
new_ext='pickle')
self.img_object.int_file = os.path.join(self.img_object.int_path, fname)
# Processing log path for image
self.img_object.log_path = util.make_image_path(self.img_object.img_path,
input_base, log_base)
fname = util.make_filename(prefix=image_index,
path=self.img_object.img_path,
new_ext='log')
self.img_object.int_log = os.path.join(self.img_object.log_path, fname)
# DIALS log path for image
if dials_log_base:
self.img_object.dials_log_path = util.make_image_path(
self.img_object.img_path, input_base, dials_log_base)
fname = util.make_filename(prefix=image_index,
path=self.img_object.img_path,
new_ext='log')
self.img_object.dials_log = os.path.join(
self.img_object.dials_log_path, fname)
# Visualization path (may need to deprecate)
self.img_object.viz_path = util.make_image_path(self.img_object.img_path,
input_base, viz_base)
fname = util.make_filename(prefix='int',
suffix=image_index,
path=self.img_object.img_path,
new_ext='png')
self.viz_file = os.path.join(self.img_object.viz_path, fname)
# Make paths if they don't exist already
for path in [self.img_object.obj_path, self.img_object.int_path,
self.img_object.log_path, self.img_object.viz_path,
self.img_object.dials_log_path]:
try:
os.makedirs(path)
except OSError:
pass
# Populate the 'final' dictionary
self.img_object.final['final'] = self.img_object.int_file
self.img_object.final['img'] = self.img_object.img_path
def process(self, img_object, single_image=False):
""" Image processing; selects method, runs requisite modules """
self.img_object = img_object
if self.img_object.status != 'bypass grid search':
self.img_object.status = 'processing'
#for CCTBX indexing / integration
terminate = False
prev_status = self.img_object.status
prev_fail = 'first cycle'
prev_final = self.img_object.final
prev_epv = 9999
while not terminate:
# Run grid search if haven't already
if (self.img_object.fail is None
and 'grid search' not in self.img_object.status):
self.integrate_cctbx('grid search', single_image=single_image)
# Run selection if haven't already
if (self.img_object.fail is None
and self.img_object.status != 'selection'):
self.select_cctbx()
# If smart grid search is active run multiple rounds until convergence
if self.params.cctbx_ha14.grid_search.type == 'smart':
if (self.img_object.fail is None
and self.img_object.final['epv'] < prev_epv):
prev_epv = self.img_object.final['epv']
prev_final = self.img_object.final
prev_status = self.img_object.status
prev_fail = self.img_object.fail
self.hmed = self.img_object.final['sph']
self.amed = self.img_object.final['spa']
self.img_object.generate_grid()
self.img_object.final['final'] = self.img_object.int_file
if len(self.img_object.grid) == 0:
self.img_object.final = prev_final
self.img_object.status = prev_status
self.img_object.fail = prev_fail
terminate = True
continue
if self.verbose:
log_entry = '\nNew starting point: H = {}, A = {}\n'\
''.format(self.hmed, self.amed)
self.img_object.log_info.append(log_entry)
else:
if prev_fail != 'first cycle':
self.img_object.final = prev_final
self.img_object.status = prev_status
self.img_object.fail = prev_fail
if self.verbose:
log_entry = '\nFinal set of parameters: H = {}, A = {}'\
''.format(self.img_object.final['sph'],
self.img_object.final['spa'])
self.img_object.log_info.append(log_entry)
terminate = True
# If brute force grid search is selected run one round
else:
terminate = True
# Run final integration if haven't already
if self.img_object.fail is None and self.img_object.status != 'final':
self.integrate_cctbx('integrate', single_image=single_image)
# If verbose output selected (default), write to main log
if self.verbose:
log_entry = "\n".join(self.img_object.log_info)
util.main_log(self.init.logfile, log_entry)
util.main_log(self.init.logfile, '\n\n')
# Make a temporary process log into a final process log
if os.path.isfile(self.img_object.int_log):
l_fname = util.make_filename(self.img_object.int_log,
new_ext='log')
final_int_log = os.path.join(self.img_object.log_path, l_fname)
os.rename(self.img_object.int_log, final_int_log)
# Save results into a pickle file
self.img_object.status = 'final'
from libtbx import easy_pickle as ep
ep.dump(self.img_object.obj_file, self.img_object)
return self.img_object