def save_data_as(self):
if self.new_fname is not None and self.new_fname != "":
with self.file_lock:
with catch(self.sphere.data_file, 'r') as f1:
with catch(self.new_fname, 'w') as f2:
for key in f1:
f1.copy(key, f2)
for attr in f1.attrs:
f2.attrs[attr] = f1.attrs[attr]
self.new_fname = None
def bai_2d_all(self):
"""Integrates all arches 2d. Note, does not call sphere method
directly, handles same functions but broken up for updates
after each image.
"""
self.data_2d.clear()
with self.sphere.sphere_lock:
if self.sphere.static:
self.sphere.bai_2d = int_2d_data_static()
else:
self.sphere.bai_2d = int_2d_data()
for arch in self.sphere.arches:
if self.sphere.static:
arch.static = True
if self.sphere.gi:
arch.gi = True
arch.integrate_2d(**self.sphere.bai_2d_args)
self.sphere.arches[arch.idx] = arch
self.sphere._update_bai_2d(arch)
self.data_2d[int(arch.idx)] = {
'map_raw': arch.map_raw,
'mask': arch.mask,
'int_2d': arch.int_2d
}
self.update.emit(arch.idx)
with self.file_lock:
with catch(self.sphere.data_file, 'a') as file:
ut.dict_to_h5(self.sphere.bai_2d_args, file, 'bai_2d_args')
def load_arches_data(self, arch_ids, load_2d):
"""Loads data from hdf5 file and sets attributes.
args:
file: h5py file or group object
"""
# ic()
with catch(self.sphere.data_file, 'r') as file:
# ic(arch_ids)
for idx in arch_ids:
try:
# ic(idx)
arch = EwaldArch(idx=idx, static=True, gi=self.sphere.gi)
if not load_2d:
# arch.load_from_h5(file['arches'], load_2d=False)
self.load_arch_data(file['arches'],
arch,
idx,
load_2d=False)
self.data_1d[int(idx)] = arch.copy(include_2d=False)
# ic('loaded 1D data', self.data_1d.keys())
else:
try:
if len(arch.int_2d.i_qChi) == 0:
pass
except TypeError:
arch.load_from_h5(file['arches'], load_2d=True)
self.data_1d[int(idx)] = arch.copy(include_2d=False)
self.data_2d[int(idx)] = {
'map_raw': arch.map_raw,
'mask': arch.mask,
'int_2d': arch.int_2d
}
# ic('loaded 1 and 2D data', self.data_1d.keys(), self.data_2d.keys())
# ic(idx, self.arches['add_idxs'], self.arches['sub_idxs'])
if idx in self.arches['add_idxs']:
self.arches['sum_int_2d'] += self.data_2d[int(
idx)]['int_2d']
self.arches['sum_map_raw'] += self.data_2d[int(
idx)]['map_raw']
elif idx in self.arches['sub_idxs']:
self.arches['sum_int_2d'] -= self.data_2d[int(
idx)]['int_2d']
self.arches['sum_map_raw'] -= self.data_2d[int(
idx)]['map_raw']
except KeyError:
pass
def __getitem__(self, idx):
"""Initializes a new EwaldArch object and loads data from file
into it.
"""
if idx in self.index:
arch = EwaldArch(idx, static=self.static, gi=self.gi)
# invoke the lock to prevent conflicts
with self.file_lock:
# use catch to avoid oserrors which will resolve with time.
with catch(self.data_file, 'r') as f:
arch.load_from_h5(f['arches'])
return arch
else:
raise KeyError(f"Arch not found with {idx} index")
def __setitem__(self, idx, arch):
"""Sets the arch at location idx to be the new arch. If an arch
is stored with the same idx, replaces the data with the new
data.
"""
# invoke the lock to prevent conflicts
with self.file_lock:
# use catch to avoid oserrors which will resolve with time.
with catch(self.data_file, 'a') as f:
if 'arches' not in f:
f.create_group('arches')
if idx != arch.idx:
arch.idx = idx
arch.save_to_h5(f['arches'])
if arch.idx not in self.index:
self.index.append(arch.idx)
def bai_2d_all(self):
"""Integrates all arches 2d. Note, does not call sphere method
directly, handles same functions but broken up for updates
after each image.
"""
with self.sphere.sphere_lock:
self.sphere.bai_2d = int_2d_data()
for arch in self.sphere.arches:
arch.integrate_2d(**self.sphere.bai_2d_args,
global_mask=self.sphere.global_mask)
# self.sphere.arches[arch.idx] = arch
self.sphere._update_bai_2d(arch)
self.update.emit(arch.idx)
with self.file_lock:
with catch(self.sphere.data_file, 'a') as file:
ut.dict_to_h5(self.sphere.bai_2d_args, file, 'bai_2d_args')
def load_arches(self):
# ic()
with self.file_lock:
with catch(self.sphere.data_file, 'r') as file:
# ic(self.arch_ids)
for idx in self.arch_ids:
try:
# ic(idx)
arch = EwaldArch(idx=idx,
static=True,
gi=self.sphere.gi)
arch.load_from_h5(file['arches'],
load_2d=self.update_2d)
self.data_1d[int(idx)] = arch.copy(include_2d=False)
# ic('loaded 1D data', self.data_1d.keys())
if self.update_2d:
try:
if len(arch.int_2d.i_qChi) == 0:
pass
except TypeError:
arch.load_from_h5(file['arches'],
load_2d=self.update_2d)
self.data_2d[int(idx)] = {
'map_raw': arch.map_raw,
'mask': arch.mask,
'int_2d': arch.int_2d
}
if idx in self.arches['add_idxs']:
self.arches['sum_int_2d'] += self.data_2d[int(
idx)]['int_2d']
self.arches['sum_map_raw'] += self.data_2d[int(
idx)]['map_raw']
elif idx in self.arches['sub_idxs']:
self.arches['sum_int_2d'] -= self.data_2d[int(
idx)]['int_2d']
self.arches['sum_map_raw'] -= self.data_2d[int(
idx)]['map_raw']
except KeyError:
pass
# ic(self.data_1d.keys(), self.data_2d.keys(), self.arches.keys())
self.sigUpdate.emit()
gc.collect()
def _set_new_mask(self, idx, mask):
mask_ids = np.arange(self.mask_widget.data.size)[mask.ravel() == 1]
if idx < 0:
self.sphere.global_mask = mask_ids
with self.sphere.file_lock:
self.sphere.save_to_h5()
else:
if self.arch.idx is not None and self.arch.idx == idx:
_arch = self.arch
else:
try:
with self.sphere.file_lock:
_arch = self.sphere.arches[idx]
except KeyError:
traceback.print_exc()
return
_arch.mask = mask_ids
with self.sphere.file_lock:
with catch(self.sphere.data_file, 'a') as file:
arches = file['arches']
_arch.save_to_h5(arches)
def __init__(self, data_file, file_lock, arches=[],
static=False, gi=False):
"""data_file: Path to hdf5 file for storing data.
file_lock: Thread safe lock.
arches: List of arches to initialize series with.
"""
self.data_file = data_file
self.file_lock = file_lock
self.index = []
self.static = static
self.gi = gi
if arches:
for a in arches:
self.__setitem__(a.idx, a)
self._i = 0
# invoke the lock to prevent conflicts
with self.file_lock:
# use catch to avoid oserrors which will resolve with time.
with catch(self.data_file, 'a') as f:
if 'arches' not in f:
f.create_group('arches')
def load_arch(self):
with self.file_lock:
with catch(self.sphere.data_file, 'r') as file:
self.arch.load_from_h5(file['arches'])
self.sigUpdate.emit()