def build_display_table_lines(self):
unfixed_samp_constraints = list(samp_constraints)
for name in self._fixed_samp_constraints:
unfixed_samp_constraints.remove(name)
if self._hide_detector_constraint:
constraint_types = (ref_constraints, unfixed_samp_constraints)
else:
constraint_types = (det_constraints, ref_constraints,
unfixed_samp_constraints)
num_rows = max([len(col) for col in constraint_types])
max_name_width = max(
[len(name) for name in sum(constraint_types[:-1], ())])
cells = []
header_cells = []
if not self._hide_detector_constraint:
header_cells.append(bold(' ' + 'DET'.ljust(max_name_width)))
header_cells.append(bold(' ' + 'REF'.ljust(max_name_width)))
header_cells.append(bold(' ' + 'SAMP'))
cells.append(header_cells)
underline_cells = [' ' + '-' * max_name_width] * len(constraint_types)
cells.append(underline_cells)
for n_row in range(num_rows):
row_cells = []
for col in constraint_types:
name = col[n_row] if n_row < len(col) else ''
row_cells.append(self._label_constraint(name))
row_cells.append(('%-' + str(max_name_width) + 's') % name)
cells.append(row_cells)
lines = [' '.join(row_cells).rstrip() for row_cells in cells]
return lines
def __str__(self):
if self._state.name is None:
return "<<< No UB calculation started >>>"
lines = []
lines.append(bold("UBCALC"))
lines.append("")
lines.append(" name:".ljust(WIDTH) + self._state.name.rjust(9))
if self.include_sigtau:
lines.append("")
lines.append(" sigma:".ljust(WIDTH) +
("% 9.5f" % self._state.sigma).rjust(9))
lines.append(" tau:".ljust(WIDTH) +
("% 9.5f" % self._state.tau).rjust(9))
if self.include_reference:
lines.append("")
ub_calculated = self._UB is not None
lines.extend(
self._state.reference.repr_lines(ub_calculated, WIDTH,
self._ROT))
lines.append("")
lines.append(bold("CRYSTAL"))
lines.append("")
if self._state.crystal is None:
lines.append(" <<< none specified >>>")
else:
lines.extend(self._state.crystal.str_lines())
lines.append("")
lines.append(bold("UB MATRIX"))
lines.append("")
if self._UB is None:
lines.append(" <<< none calculated >>>")
else:
lines.extend(self.str_lines_u())
lines.append("")
lines.extend(self.str_lines_u_angle_and_axis())
lines.append("")
lines.extend(self.str_lines_ub())
lines.append("")
lines.append(bold("REFLECTIONS"))
lines.append("")
lines.extend(self._state.reflist.str_lines())
lines.append("")
lines.append(bold("CRYSTAL ORIENTATIONS"))
lines.append("")
lines.extend(self._state.orientlist.str_lines(R=self._ROT))
return '\n'.join(lines)
def __str__(self):
if self._state.name is None:
return "<<< No UB calculation started >>>"
lines = []
lines.append(bold("UBCALC"))
lines.append("")
lines.append(" name:".ljust(WIDTH) + self._state.name.rjust(9))
if self.include_sigtau:
lines.append("")
lines.append(" sigma:".ljust(WIDTH) +
("% 9.5f" % self._state.sigma).rjust(9))
lines.append(" tau:".ljust(WIDTH) +
("% 9.5f" % self._state.tau).rjust(9))
_ub_calculated = self._UB is not None
if self.include_reference:
lines.append("")
lines.append(bold("REFERNCE"))
lines.append("")
lines.extend(
self._state.reference.repr_lines(_ub_calculated, WIDTH,
self._tobj))
lines.append("")
lines.append(bold("SURFACE NORMAL"))
lines.append("")
lines.extend(
self._state.surface.repr_lines(_ub_calculated, WIDTH, self._tobj))
lines.append("")
lines.append(bold("CRYSTAL"))
lines.append("")
if self._state.crystal is None:
lines.append(" <<< none specified >>>")
else:
lines.extend(self._state.crystal.str_lines(self._tobj))
lines.append("")
lines.append(bold("UB MATRIX"))
lines.append("")
if self._UB is None:
lines.append(" <<< none calculated >>>")
else:
lines.extend(self.str_lines_u(self.U))
lines.append("")
lines.extend(self.str_lines_ub_angle_and_axis(self.UB))
lines.append("")
lines.extend(self.str_lines_ub(self.UB))
lines.extend(self.str_lines_refl())
lines.extend(self.str_lines_orient())
return '\n'.join(lines)
def __str__(self):
if self._state.name is None:
return "<<< No UB calculation started >>>"
lines = []
lines.append(bold("UBCALC"))
lines.append("")
lines.append(
" name:".ljust(WIDTH) + self._state.name.rjust(9))
if self.include_sigtau:
lines.append("")
lines.append(
" sigma:".ljust(WIDTH) + ("% 9.5f" % self._state.sigma).rjust(9))
lines.append(
" tau:".ljust(WIDTH) + ("% 9.5f" % self._state.tau).rjust(9))
if self.include_reference:
lines.append("")
ub_calculated = self._UB is not None
lines.extend(self._state.reference.repr_lines(ub_calculated, WIDTH))
lines.append("")
lines.append(bold("CRYSTAL"))
lines.append("")
if self._state.crystal is None:
lines.append(" <<< none specified >>>")
else:
lines.extend(self._state.crystal.str_lines())
lines.append("")
lines.append(bold("UB MATRIX"))
lines.append("")
if self._UB is None:
lines.append(" <<< none calculated >>>")
else:
lines.extend(self.str_lines_u())
lines.append("")
lines.extend(self.str_lines_u_angle_and_axis())
lines.append("")
lines.extend(self.str_lines_ub())
lines.append("")
lines.append(bold("REFLECTIONS"))
lines.append("")
lines.extend(self._state.reflist.str_lines())
return '\n'.join(lines)
def format_command_help(command_list):
row_list = _command_list_to_table_cells(command_list)
lines = []
for row_cells in row_list:
if len(row_cells) == 1:
heading = row_cells[0]
lines.append('')
lines.append(bold(heading))
lines.append('')
elif len(row_cells) == 2:
cell1, cell2 = row_cells
cell1_lines = textwrap.wrap(cell1, WIDTH, subsequent_indent=' ')
cell2_lines = textwrap.wrap(cell2, 79 - INDENT - 3 - WIDTH)
first_line = True
while cell1_lines or cell2_lines:
line = ' ' * INDENT
if cell1_lines:
line += cell1_lines.pop(0).ljust(WIDTH)
else:
line += ' ' * (WIDTH)
line += ' : ' if first_line else ' '
if cell2_lines:
line += cell2_lines.pop(0)
lines.append(line)
first_line = False
return '\n'.join(lines)
def str_lines(self, R=None):
if not self._orientlist:
return [" <<< none specified >>>"]
lines = []
str_format = (" %5s %5s %5s %5s %5s %5s TAG")
values = ('H', 'K', 'L', 'X', 'Y', 'Z')
lines.append(bold(str_format % values))
for n in range(len(self._orientlist)):
orient_tuple = self.getOrientation(n + 1)
[h, k, l], [x, y, z], tag, _ = orient_tuple
try:
xyz_rot = R.I * matrix([[x],[y],[z]])
xr, yr, zr = xyz_rot.T.tolist()[0]
except AttributeError:
xr, yr, zr = x ,y ,z
if tag is None:
tag = ""
str_format = (" %2d % 4.2f % 4.2f % 4.2f " +
"% 4.2f % 4.2f % 4.2f %s")
values = (n + 1, h, k, l, xr, yr, zr, tag)
lines.append(str_format % values)
return lines
def format_command_help(command_list):
row_list = _command_list_to_table_cells(command_list)
lines = []
for row_cells in row_list:
if len(row_cells) == 1:
heading = row_cells[0]
lines.append('')
lines.append(bold(heading))
lines.append('')
elif len(row_cells) == 2:
cell1, cell2 = row_cells
cell1_lines = textwrap.wrap(cell1, WIDTH, subsequent_indent=' ')
cell2_lines = textwrap.wrap(cell2, 79 - INDENT - 3 - WIDTH)
first_line = True
while cell1_lines or cell2_lines:
line = ' ' * INDENT
if cell1_lines:
line += cell1_lines.pop(0).ljust(WIDTH)
else:
line += ' ' * (WIDTH)
line += ' : ' if first_line else ' '
if cell2_lines:
line += cell2_lines.pop(0)
lines.append(line)
first_line = False
return '\n'.join(lines)
def str_lines(self, conv=None):
axes = tuple(s.upper() for s in self._externalAngleNames)
if not self._orientlist:
return [" <<< none specified >>>"]
lines = []
str_format = (" %5s %5s %5s %5s %5s %5s " + "%8s " * len(axes) +
" TAG")
values = ('H', 'K', 'L', 'X', 'Y', 'Z') + axes
lines.append(bold(str_format % values))
for n in range(1, len(self._orientlist) + 1):
orient_tuple = self.get_orientation_in_external_angles(n)
[h, k, l], [x, y, z], externalAngles, tag, _ = orient_tuple
try:
xyz_rot = conv.transform(matrix([[x], [y], [z]]), True)
xr, yr, zr = xyz_rot.T.tolist()[0]
except AttributeError:
xr, yr, zr = x, y, z
if tag is None:
tag = ""
str_format = (" %2d % 4.2f % 4.2f % 4.2f " +
"% 4.2f % 4.2f % 4.2f " + "% 8.4f " * len(axes) +
" %s")
values = (n, h, k, l, xr, yr, zr) + externalAngles + (tag, )
lines.append(str_format % values)
return lines
def checkub():
"""checkub -- show calculated and entered hkl values for reflections.
"""
s = "\n %7s %4s %4s %4s %6s %6s %6s TAG\n" % \
('ENERGY', 'H', 'K', 'L', 'H_COMP', 'K_COMP', 'L_COMP')
s = bold(s)
nref = ubcalc.get_number_reflections()
if not nref:
s += "<<empty>>"
for n in range(nref):
hklguess, pos, energy, tag, _ = ubcalc.get_reflection(n + 1)
wavelength = 12.39842 / energy
hkl = settings.angles_to_hkl_function(pos.inRadians(), wavelength, ubcalc.UB)
h, k, l = hkl
if tag is None:
tag = ""
s += ("% 2d % 6.4f % 4.2f % 4.2f % 4.2f % 6.4f % 6.4f "
"% 6.4f %6s\n" % (n + 1, energy, hklguess[0],
hklguess[1], hklguess[2], h, k, l, tag))
print(s)
def str_lines(self):
axes = tuple(s.upper() for s in self._externalAngleNames)
if not self._reflist:
return [" <<< none specified >>>"]
lines = []
format = (" %6s %5s %5s %5s " + "%8s " * len(axes) + " TAG")
values = ('ENERGY', 'H', 'K', 'L') + axes
lines.append(bold(format % values))
for n in range(len(self._reflist)):
ref_tuple = self.get_reflection_in_external_angles(n + 1)
[h, k, l], externalAngles, energy, tag, _ = ref_tuple
if tag is None:
tag = ""
format = (" %2d %6.3f % 4.2f % 4.2f % 4.2f " +
"% 8.4f " * len(axes) + " %s")
values = (n + 1, energy, h, k, l) + externalAngles + (tag, )
lines.append(format % values)
return lines
def checkub():
"""checkub -- show calculated and entered hkl values for reflections.
"""
s = "\n %7s %4s %4s %4s %6s %6s %6s TAG\n" % \
('ENERGY', 'H', 'K', 'L', 'H_COMP', 'K_COMP', 'L_COMP')
s = bold(s)
nref = ubcalc.get_number_reflections()
if not nref:
s += "<<empty>>"
for n in range(nref):
hklguess, pos, energy, tag, _ = ubcalc.get_reflection(n + 1)
wavelength = 12.39842 / energy
hkl = settings.angles_to_hkl_function(pos.inRadians(), wavelength, ubcalc.UB)
h, k, l = hkl
if tag is None:
tag = ""
s += ("% 2d % 6.4f % 4.2f % 4.2f % 4.2f % 6.4f % 6.4f "
"% 6.4f %6s\n" % (n + 1, energy, hklguess[0],
hklguess[1], hklguess[2], h, k, l, tag))
print s
def str_lines(self):
axes = tuple(s.upper() for s in self._externalAngleNames)
if not self._reflist:
return [" <<< none specified >>>"]
lines = []
format = (" %6s %5s %5s %5s " + "%8s " * len(axes) + " TAG")
values = ('ENERGY', 'H', 'K', 'L') + axes
lines.append(bold(format % values))
for n in range(len(self._reflist)):
ref_tuple = self.get_reflection_in_external_angles(n + 1)
[h, k, l], externalAngles, energy, tag, _ = ref_tuple
if tag is None:
tag = ""
format = (" %2d %6.3f % 4.2f % 4.2f % 4.2f " +
"% 8.4f " * len(axes) + " %s")
values = (n + 1, energy, h, k, l) + externalAngles + (tag,)
lines.append(format % values)
return lines
def print_first_point(self, position_dict):
# also sets self.widths
header_strings = []
for scn in self.scannables:
field_names = list(scn.getInputNames()) + list(scn.getExtraNames())
if len(field_names) == 1:
header_strings.append(scn.getName())
else:
for field_name in field_names:
header_strings.append(field_name)
first_row_strings = []
for scn in self.scannables:
pos = position_dict[scn]
first_row_strings.extend(scn.formatPositionFields(pos))
self.widths = []
for header, pos_string in zip(header_strings, first_row_strings):
self.widths.append(max(len(header), len(pos_string)))
header_cells = []
for heading, width in zip(header_strings, self.widths):
header_cells.append(heading.rjust(width))
underline_cells = ['-' * w for w in self.widths]
first_row_cells = []
for pos, width in zip(first_row_strings, self.widths):
first_row_cells.append(pos.rjust(width))
#table_width = sum(self.widths) + len(self.widths * 2) - 2
lines = []
#lines.append('=' * table_width)
lines.append(bold(' '.join(header_cells)))
lines.append(' '.join(underline_cells))
lines.append(' '.join(first_row_cells))
print '\n'.join(lines)
def print_first_point(self, position_dict):
# also sets self.widths
header_strings = []
for scn in self.scannables:
field_names = list(scn.getInputNames()) + list(scn.getExtraNames())
if len(field_names) == 1:
header_strings.append(scn.getName())
else:
for field_name in field_names:
header_strings.append(field_name)
first_row_strings = []
for scn in self.scannables:
pos = position_dict[scn]
first_row_strings.extend(scn.formatPositionFields(pos))
self.widths = []
for header, pos_string in zip(header_strings, first_row_strings):
self.widths.append(max(len(header), len(pos_string)))
header_cells = []
for heading, width in zip(header_strings, self.widths):
header_cells.append(heading.rjust(width))
underline_cells = ['-' * w for w in self.widths]
first_row_cells = []
for pos, width in zip(first_row_strings, self.widths):
first_row_cells.append(pos.rjust(width))
#table_width = sum(self.widths) + len(self.widths * 2) - 2
lines = []
#lines.append('=' * table_width)
lines.append(bold(' '.join(header_cells)))
lines.append(' '.join(underline_cells))
lines.append(' '.join(first_row_cells))
print '\n'.join(lines)
import diffcalc.util
import diffcalc.gdasupport.minigda.command
DIFFCALC_ROOT = os.path.realpath(diffcalc.__file__).split('diffcalc/__init__.py')[0]
try:
__IPYTHON__ # @UndefinedVariable
IPYTHON = True
except NameError:
IPYTHON = False
module_name = sys.argv[1] #3 if IPYTHON else 1]
debug = sys.argv[2] == 'True' #4 if IPYTHON else 2])
print
print bold('-' * 34 + ' DIFFCALC ' + '-' * 35)
# configure persisentence
DIFFCALC_VAR = os.path.join(os.path.expanduser('~'), '.diffcalc', module_name)
if not os.path.exists(DIFFCALC_VAR):
print "Making diffcalc var folder:'%s'" % DIFFCALC_VAR
os.makedirs(DIFFCALC_VAR)
diffcalc.settings.ubcalc_persister = UBCalculationJSONPersister(DIFFCALC_VAR)
# configure debug
diffcalc.util.DEBUG = debug
if debug:
print "WARNING: debug mode on; help for command syntax errors disabled."
# import script
script = os.path.join(DIFFCALC_ROOT, 'startup', module_name) + '.py'
import diffcalc.util
import diffcalc.gdasupport.minigda.command
DIFFCALC_ROOT = os.path.realpath(
diffcalc.__file__).split('diffcalc/__init__.py')[0]
try:
__IPYTHON__ # @UndefinedVariable
IPYTHON = True
except NameError:
IPYTHON = False
module_name = sys.argv[1] #3 if IPYTHON else 1]
debug = sys.argv[2] == 'True' #4 if IPYTHON else 2])
print
print(bold('-' * 34 + ' DIFFCALC ' + '-' * 35))
# configure persisentence
DIFFCALC_VAR = os.path.join(os.path.expanduser('~'), '.diffcalc', module_name)
if not os.path.exists(DIFFCALC_VAR):
print("Making diffcalc var folder:'%s'" % DIFFCALC_VAR)
os.makedirs(DIFFCALC_VAR)
diffcalc.settings.ubcalc_persister = UBCalculationJSONPersister(
DIFFCALC_VAR, UBCalcStateEncoder)
# configure debug
diffcalc.util.DEBUG = debug
if debug:
print("WARNING: debug mode on; help for command syntax errors disabled.")
# import script
from diffcalc.util import bold
import diffcalc.util
DIFFCALC_ROOT = os.path.realpath(diffcalc.__file__).split('diffcalc/__init__.py')[0]
try:
__IPYTHON__ # @UndefinedVariable
IPYTHON = True
except NameError:
IPYTHON = False
module_name = sys.argv[1] #3 if IPYTHON else 1]
debug = sys.argv[2] == 'True' #4 if IPYTHON else 2])
print
print bold('-' * 34 + ' DIFFCALC ' + '-' * 35)
# configure persisentence
DIFFCALC_VAR = os.path.join(os.path.expanduser('~'), '.diffcalc', module_name)
if not os.path.exists(DIFFCALC_VAR):
print "Making diffcalc var folder:'%s'" % DIFFCALC_VAR
os.makedirs(DIFFCALC_VAR)
diffcalc.settings.ubcalc_persister = UBCalculationJSONPersister(DIFFCALC_VAR)
# configure debug
diffcalc.util.DEBUG = debug
if debug:
print "WARNING: debug mode on; help for command syntax errors disabled."
# import script
script = os.path.join(DIFFCALC_ROOT, 'startup', module_name) + '.py'
def str_lines_orient(self):
lines = ["", bold("CRYSTAL ORIENTATIONS"), ""]
lines.extend(self._state.orientlist.str_lines(self._tobj))
return lines
def str_lines_refl(self):
lines = ["", bold("REFLECTIONS"), ""]
lines.extend(self._state.reflist.str_lines())
return lines
