本文整理汇总了Python中xia2.lib.bits.auto_logfiler函数的典型用法代码示例。如果您正苦于以下问题:Python auto_logfiler函数的具体用法?Python auto_logfiler怎么用?Python auto_logfiler使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了auto_logfiler函数的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: Sortmtz
def Sortmtz(self):
'''Create a Sortmtz wrapper from _Sortmtz - set the working directory
and log file stuff as a part of this...'''
sortmtz = _Sortmtz()
sortmtz.set_working_directory(self.get_working_directory())
auto_logfiler(sortmtz)
return sortmtz
示例2: get_reciprocal_space_primitive_matrix
def get_reciprocal_space_primitive_matrix(lattice, matrix, wd = None):
'''Get the primitive reciprocal space vectors for this matrix.'''
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
new_cell = o.get_cell('aP')
op = symop_to_mat(o.get_reindex_op('aP'))
primitive_a = matmul(invert(op), a)
return mat2vec(primitive_a)
示例3: Chef
def Chef(self):
'''Create a Chef wrapper from _Chef - set the
working directory and log file stuff as a part of this...'''
chef = _Chef()
chef.set_working_directory(self.get_working_directory())
auto_logfiler(chef)
return chef
示例4: Report
def Report(self):
report = _Report()
report.set_working_directory(self.get_working_directory())
report.set_experiments_filename(self._intgr_experiments_filename)
report.set_reflections_filename(self._intgr_integrated_pickle)
auto_logfiler(report, 'REPORT')
return report
示例5: Freerflag
def Freerflag(self):
'''Create a Freerflag wrapper from _Freerflag - set the working
directory and log file stuff as a part of this...'''
freerflag = _Freerflag()
freerflag.set_working_directory(self.get_working_directory())
auto_logfiler(freerflag)
return freerflag
示例6: Matthews_coef
def Matthews_coef(self):
'''Create a Matthews_coef wrapper from _Matthews_coef - set the
working directory and log file stuff as a part of this...'''
matthews_coef = _Matthews_coef()
matthews_coef.set_working_directory(self.get_working_directory())
auto_logfiler(matthews_coef)
return matthews_coef
示例7: Mtz2various
def Mtz2various(self):
'''Create a Mtz2various wrapper from _Mtz2various - set the working
directory and log file stuff as a part of this...'''
mtz2various = _Mtz2various()
mtz2various.set_working_directory(self.get_working_directory())
auto_logfiler(mtz2various)
return mtz2various
示例8: Cad
def Cad(self):
'''Create a Cad wrapper from _Cad - set the working directory
and log file stuff as a part of this...'''
cad = _Cad()
cad.set_working_directory(self.get_working_directory())
auto_logfiler(cad)
return cad
示例9: Reindex
def Reindex(self):
'''Create a Reindex wrapper from _Reindex - set the working directory
and log file stuff as a part of this...'''
reindex = _Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
return reindex
示例10: _index_select_images
def _index_select_images(self):
'''Select correct images based on image headers. This will in
general use the 20 frames. N.B. only if they have good
spots on them!'''
phi_width = self.get_phi_width()
images = self.get_matching_images()
# N.B. now bodging this to use up to 20 frames which have decent
# spots on, spaced from throughout the data set.
spacing = max(1, int(len(images) // 20))
selected = []
for j in range(0, len(images), spacing):
selected.append(images[j])
for image in selected[:20]:
ld = LabelitDistl()
ld.set_working_directory(self.get_working_directory())
auto_logfiler(ld)
ld.add_image(self.get_image_name(image))
ld.distl()
spots = ld.get_statistics(
self.get_image_name(image))['spots_good']
Debug.write('Image %d good spots %d' % (image, spots))
if spots > 10:
self.add_indexer_image_wedge(image)
return
示例11: Idxref
def Idxref(self):
from xia2.Handlers.Phil import PhilIndex
idxref = _Idxref(params=PhilIndex.params.xds.index)
idxref.set_working_directory(self.get_working_directory())
idxref.setup_from_imageset(self.get_imageset())
if self.get_distance():
idxref.set_distance(self.get_distance())
if self.get_wavelength():
idxref.set_wavelength(self.get_wavelength())
# if we have a refined set of parameters to apply, apply these
if Flags.get_xparm():
idxref.set_refined_origin(Flags.get_xparm_origin())
idxref.set_refined_beam_vector(Flags.get_xparm_beam_vector())
idxref.set_refined_rotation_axis(Flags.get_xparm_rotation_axis())
idxref.set_refined_distance(Flags.get_xparm_distance())
# hacks for Jira 493
if Flags.get_xparm_a():
idxref.set_a_axis(Flags.get_xparm_a())
if Flags.get_xparm_b():
idxref.set_b_axis(Flags.get_xparm_b())
if Flags.get_xparm_c():
idxref.set_c_axis(Flags.get_xparm_c())
auto_logfiler(idxref, 'IDXREF')
return idxref
示例12: get_real_space_primitive_matrix
def get_real_space_primitive_matrix(lattice, matrix, wd = None):
'''Get the primitive real space vectors for the unit cell and
lattice type. Note that the resulting matrix will need to be
scaled by a factor equal to the wavelength in Angstroms.'''
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
new_cell = o.get_cell('aP')
op = symop_to_mat(o.get_reindex_op('aP'))
primitive_a = matmul(invert(op), a)
# then convert to real space
real_a = invert(primitive_a)
return real_a[0:3], real_a[3:6], real_a[6:9]
示例13: Scaleit
def Scaleit(self):
'''Create a Scaleit wrapper from _Scaleit - set the working directory
and log file stuff as a part of this...'''
scaleit = _Scaleit()
scaleit.set_working_directory(self.get_working_directory())
auto_logfiler(scaleit)
return scaleit
示例14: Mtzdump
def Mtzdump(self):
'''Create a Mtzdump wrapper from _Mtzdump - set the working directory
and log file stuff as a part of this...'''
mtzdump = _Mtzdump()
mtzdump.set_working_directory(self.get_working_directory())
auto_logfiler(mtzdump)
return mtzdump
示例15: Correct
def Correct(self):
correct = _Correct(params=PhilIndex.params.xds.correct)
correct.set_working_directory(self.get_working_directory())
correct.setup_from_imageset(self.get_imageset())
if self.get_distance():
correct.set_distance(self.get_distance())
if self.get_wavelength():
correct.set_wavelength(self.get_wavelength())
if self.get_integrater_ice():
correct.set_ice(self.get_integrater_ice())
if self.get_integrater_excluded_regions():
correct.set_excluded_regions(self.get_integrater_excluded_regions())
if self.get_integrater_anomalous():
correct.set_anomalous(True)
if self.get_integrater_low_resolution() > 0.0:
Debug.write('Using low resolution limit: %.2f' % \
self.get_integrater_low_resolution())
correct.set_resolution_high(0.0)
correct.set_resolution_low(
self.get_integrater_low_resolution())
auto_logfiler(correct, 'CORRECT')
return correct