def OnRestoreMetrology(self, event):
print("Not implemented")
return
dialog = wx.FileDialog(
self,
defaultDir="",
message="Restore metrology file",
style=wx.FD_OPEN,
wildcard="Phil files (*.eff; *.def)|*.eff;*.def")
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
if (path != ""):
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
from libtbx import phil
frame = self.GetParent().GetParent()
stream = open(path)
metrology_phil = master_phil.fetch(
sources=[phil.parse(stream.read())])
stream.close()
# Merge restored metrology into the raw image
from libtbx.phil import experimental
experimental.merge_params_by_key(
frame.pyslip.tiles.raw_image._metrology_params,
metrology_phil.extract(), 'serial')
img = frame.pyslip.tiles.raw_image
img.apply_metrology_from_matrices(
metrology_as_transformation_matrices(
metrology_phil.extract()))
# Update the view, trigger redraw. XXX Duplication
# w.r.t. OnUpdateQuad().
tiles = frame.pyslip.tiles
tiles.flex_image = frame.pyslip.tiles.raw_image.get_flex_image(
brightness=tiles.current_brightness / 100)
tiles.flex_image.adjust(
color_scheme=tiles.current_color_scheme)
tiles.reset_the_cache()
tiles.tile_cache = tiles.cache[tiles.zoom_level]
tiles.tile_list = tiles.lru[tiles.zoom_level]
frame.pyslip.Update()
# Update the controls, remember to reset the default values
# for the spinners.
for serial in range(4):
fast, slow = img.get_panel_fast_slow(serial)
name_quadrant = ["Q0", "Q1", "Q2", "Q3"][serial]
spinner = getattr(self, "_" + name_quadrant + "_fast_ctrl")
spinner.SetDefaultValue(fast)
spinner.SetValue(fast)
spinner = getattr(self, "_" + name_quadrant + "_slow_ctrl")
spinner.SetDefaultValue(slow)
spinner.SetValue(slow)
def OnRestoreMetrology(self, event):
print "Not implemented"
return
dialog = wx.FileDialog(
self,
defaultDir="",
message="Restore metrology file",
style=wx.FD_OPEN,
wildcard="Phil files (*.eff; *.def)|*.eff;*.def")
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
if (path != "") :
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
from libtbx import phil
frame = self.GetParent().GetParent()
stream = open(path)
metrology_phil = master_phil.fetch(sources=[phil.parse(stream.read())])
stream.close()
# Merge restored metrology into the raw image
from libtbx.phil import experimental
experimental.merge_params_by_key(
frame.pyslip.tiles.raw_image._metrology_params,
metrology_phil.extract(),
'serial')
img = frame.pyslip.tiles.raw_image
img.apply_metrology_from_matrices(metrology_as_transformation_matrices(
metrology_phil.extract()))
# Update the view, trigger redraw. XXX Duplication
# w.r.t. OnUpdateQuad().
tiles = frame.pyslip.tiles
tiles.flex_image = frame.pyslip.tiles.raw_image.get_flex_image(
brightness=tiles.current_brightness / 100)
tiles.flex_image.adjust(color_scheme=tiles.current_color_scheme)
tiles.reset_the_cache()
tiles.tile_cache = tiles.cache[tiles.zoom_level]
tiles.tile_list = tiles.lru[tiles.zoom_level]
frame.pyslip.Update()
# Update the controls, remember to reset the default values
# for the spinners.
for serial in xrange(4):
fast, slow = img.get_panel_fast_slow(serial)
name_quadrant = ["Q0", "Q1", "Q2", "Q3"][serial]
spinner = getattr(self, "_" + name_quadrant + "_fast_ctrl")
spinner.SetDefaultValue(fast)
spinner.SetValue(fast)
spinner = getattr(self, "_" + name_quadrant + "_slow_ctrl")
spinner.SetDefaultValue(slow)
spinner.SetValue(slow)
def transformation_matrices_as_metrology(self):
"""The transformation_matrices_as_metrology() function regularizes
the the transformation matrices and converts them to a phil
object.
"""
from libtbx import phil
from xfel.cftbx.detector.metrology import \
master_phil, regularize_transformation_matrices
# XXX Experimental!
regularize_transformation_matrices(self._matrices)
(Tf_d, Tb_d) = self._matrices[(0, )]
metrology_str = "detector {\n"
metrology_str += "serial = %d\n" % 0
metrology_str += self._matrix_as_string(Tb_d)
for p in [
k[1] for k in self._matrices.keys()
if (len(k) == 2 and k[0:1] == (0, ))
]:
(Tf_p, Tb_p) = self._matrices[(0, p)]
metrology_str += "panel {\n"
metrology_str += "serial = %d\n" % p
metrology_str += self._matrix_as_string(Tf_d * Tb_p)
for s in [
k[2] for k in self._matrices.keys()
if (len(k) == 3 and k[0:2] == (0, p))
]:
(Tf_s, Tb_s) = self._matrices[(0, p, s)]
metrology_str += "sensor {\n"
metrology_str += "serial = %d\n" % s
metrology_str += self._matrix_as_string(Tf_p * Tb_s)
for a in [
k[3] for k in self._matrices.keys()
if (len(k) == 4 and k[0:3] == (0, p, s))
]:
(Tf_a, Tb_a) = self._matrices[(0, p, s, a)]
metrology_str += "asic {\n"
metrology_str += "serial = %d\n" % a
metrology_str += self._matrix_as_string(Tf_s * Tb_a)
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
return master_phil.fetch(sources=[phil.parse(metrology_str)])
def transformation_matrices_as_metrology(self):
"""The transformation_matrices_as_metrology() function regularizes
the the transformation matrices and converts them to a phil
object.
"""
from libtbx import phil
from xfel.cftbx.detector.metrology import \
master_phil, regularize_transformation_matrices
# XXX Experimental!
regularize_transformation_matrices(self._matrices)
(Tf_d, Tb_d) = self._matrices[(0,)]
metrology_str = "detector {\n"
metrology_str += "serial = %d\n" % 0
metrology_str += self._matrix_as_string(Tb_d)
for p in [k[1] for k in self._matrices.keys()
if (len(k) == 2 and k[0:1] == (0,))]:
(Tf_p, Tb_p) = self._matrices[(0, p)]
metrology_str += "panel {\n"
metrology_str += "serial = %d\n" % p
metrology_str += self._matrix_as_string(Tf_d * Tb_p)
for s in[k[2] for k in self._matrices.keys()
if (len(k) == 3 and k[0:2] == (0, p))]:
(Tf_s, Tb_s) = self._matrices[(0, p, s)]
metrology_str += "sensor {\n"
metrology_str += "serial = %d\n" % s
metrology_str += self._matrix_as_string(Tf_p * Tb_s)
for a in [k[3] for k in self._matrices.keys()
if (len(k) == 4 and k[0:3] == (0, p, s))]:
(Tf_a, Tb_a) = self._matrices[(0, p, s, a)]
metrology_str += "asic {\n"
metrology_str += "serial = %d\n" % a
metrology_str += self._matrix_as_string(Tf_s * Tb_a)
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
return master_phil.fetch(sources=[phil.parse(metrology_str)])
def sections2phil(sections, verbose):
from xfel.cftbx.detector.metrology import master_phil
# Properties of CSPad pixels (Philipp et al., 2007). The counters
# are 14 bits wide, and the pixels are square with a side length of
# 110 um. Because cspad_tbx depends on pyana, it may fail to import
# in which case a hardcoded fallback is provided.
try:
from xfel.cxi.cspad_ana.cspad_tbx import cspad_saturated_value as sv
from xfel.cxi.cspad_ana.cspad_tbx import pixel_size as ps
saturated_value = sv
pixel_size = ps * 1e-3
except ImportError:
saturated_value = 90000
pixel_size = 110e-6
# Build the Phil object. XXX Should have det-z? Probably not,
# because then it aint't just metrology anymore. In fact, under
# orthographic projection the whole translation/orientation thing
# can be scrapped for the detector. XXX look up include,
# include_scope for phil XXX Hardcoded address for now.
address = "CxiDs1-0|Cspad-0"
metrology_str = "detector { serial = %d\n" % 0
metrology_str += "label = %s\n" % address
# The center of the detector is defined as the average of all the
# sections it contains. The first coordinate of the matrix-oriented
# coordinate system of the Section class maps to -y, the second to
# x, and the third to z. While the detector still sits on the
# origin (zero translation), the mapping from the origin in Section
# coordinates is still needed.
t_d = [0, 0, 0]
nmemb = 0
for p in range(len(sections)):
for s in range(len(sections[p])):
t_d[0] += +sections[p][s].center[1]
t_d[1] += -sections[p][s].center[0]
t_d[2] += 0
nmemb += 1
if (nmemb > 0):
for i in range(3):
t_d[i] /= nmemb
metrology_str += "translation = 0, 0, 0\n"
o_d = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=0, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in o_d)
for p in range(len(sections)):
# Loop over quadrants (panels). XXX Translation of panels is
# wrongly set to to centre of sections in the quadrant
# w.r.t. center of the detector.
metrology_str += "panel { serial = %d\n" % p
metrology_str += "translation = "
t_p = [0, 0, 0]
for s in range(len(sections[p])):
t_p[0] += +sections[p][s].center[1] - t_d[0]
t_p[1] += -sections[p][s].center[0] - t_d[1]
t_p[2] += 0 - t_d[2]
for i in range(3):
t_p[i] /= len(sections[p])
metrology_str += "%s" % repr(t_p[i] * pixel_size)
if (i < 2):
metrology_str += ", "
else:
metrology_str += "\n"
# XXX Orientation wrongly set to zero.
o_p = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=0, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in o_p)
for s in range(len(sections[p])):
# Loop over sensors (sections or two-by-one:s). Note that
# sensors are rotated by -90 degrees in the SLAC metrology
# convention w.r.t. their appearance in the XTC stream.
s_t = [0, 0, 0]
s_t[0] = +sections[p][s].center[1] - t_p[0] - t_d[0]
s_t[1] = -sections[p][s].center[0] - t_p[1] - t_d[1]
s_t[2] = 0 - t_p[2] - t_d[2]
metrology_str += "sensor { serial = %d\n" % s
metrology_str += "translation = "
for i in range(3):
metrology_str += "%s" % repr(s_t[i] * pixel_size)
if (i < 2):
metrology_str += ", "
else:
metrology_str += "\n"
s_o = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=sections[p][s].angle - 90, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in s_o)
for a in range(2):
# The ASIC:s of the CSPad are 185 rows by 194 columns. The
# ASIC:s are horizontally aligned within a section, with a
# three-column gap between them.
metrology_str += "asic { serial = %d\n" % a
if (a == 0):
metrology_str += "translation = %s, %s, %s\n" % (
repr(-(194 + 3) / 2 * pixel_size), "0", "0") # XXX hardcoded!
else:
metrology_str += "translation = %s, %s, %s\n" % (
repr(+(194 + 3) / 2 * pixel_size), "0", "0") # XXX hardcoded!
metrology_str += "orientation = 1, 0, 0, 0\n"
metrology_str += "pixel_size = %s, %s\n" % (
repr(pixel_size), repr(pixel_size))
metrology_str += "dimension = %d, %d\n" % (194, 185) # XXX hardcoded!
metrology_str += "saturation = %s\n" % repr(float(saturated_value))
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_phil = master_phil.fetch(
sources=[phil.parse(metrology_str)])
return (metrology_phil)
def run(argv=None):
if (argv is None):
argv = sys.argv
# XXX Could/should handle effective metrology the same way, except
# it does not have a single scope.
work_phil = phil.process_command_line(args=argv[1:],
master_string=master_str + phil_str +
additional_spotfinder_phil_defs)
work_params = work_phil.work.extract()
app = wx.App(0)
wx.SystemOptions.SetOptionInt("osx.openfiledialog.always-show-types", 1)
frame = XrayFrame(None, -1, "X-ray image display", size=(800, 720))
frame.Show()
# show settings panel
frame.OnShowSettings(None)
frame.settings_frame.panel.center_ctrl.SetValue(work_params.beam_center)
frame.settings_frame.panel.integ_ctrl.SetValue(
work_params.show_integration_results)
frame.settings_frame.panel.spots_ctrl.SetValue(
work_params.show_spotfinder_results)
frame.settings.show_effective_tiling = work_params.show_effective_tiling
frame.settings_frame.panel.collect_values()
if (work_params.effective_metrology is not None):
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
stream = open(work_params.effective_metrology)
metrology_phil = master_phil.fetch(sources=[phil.parse(stream.read())])
stream.close()
frame.metrology_matrices = metrology_as_transformation_matrices(
metrology_phil.extract())
# Update initial settings with values from the command line. Needs
# to be done before image is loaded (but after the frame is
# instantiated).
frame.params = work_params
frame.init_pyslip()
frame.pyslip.tiles.user_requests_antialiasing = work_params.anti_aliasing
frame.pyslip.tiles.show_untrusted = frame.params.show_untrusted
paths = work_phil.remaining_args
if (len(paths) == 1 and os.path.basename(paths[0]) == "DISTL_pickle"):
assert os.path.isfile(paths[0])
frame.load_distl_output(paths[0])
elif (len(paths) > 0):
frame.CHOOSER_SIZE = 1500
# from dxtbx.imageset import ImageSetFactory
# sets = ImageSetFactory.new(paths)
from dxtbx.model.experiment_list import ExperimentListFactory
from rstbx.slip_viewer.frame import chooser_wrapper
experiments = ExperimentListFactory.from_filenames(paths)
sets = experiments.imagesets()
for imgset in sets:
for idx in imgset.indices():
frame.add_file_name_or_data(chooser_wrapper(imgset, idx))
idx = sets[0].indices()[0]
frame.load_image(chooser_wrapper(sets[0], idx))
app.MainLoop()
return 0
def metrology2phil(calib_dir, verbose):
"""XXX Should really review the SLAC progress since last time
around! XXX Note that this is all SLAC-specific (as is the whole
thing, I guess).
"""
from xfel.cftbx.detector.metrology import master_phil
# XXX Can this fail? How?
sections = calib2sections(calib_dir)
if (sections is None):
return (None)
# Properties of CSPad pixels (Philipp et al., 2007). The counters
# are 14 bits wide, and the pixels are square with a side length of
# 110 um. Because cspad_tbx depends on pyana, it may fail to import
# in which case a hardcoded fallback is provided.
try:
from xfel.cxi.cspad_ana.cspad_tbx import cspad_saturated_value as sv
from xfel.cxi.cspad_ana.cspad_tbx import pixel_size as ps
saturated_value = sv
pixel_size = ps * 1e-3
except ImportError:
saturated_value = 90000
pixel_size = 110e-6
# Build the Phil object. XXX Should have det-z? Probably not,
# because then it aint't just metrology anymore. In fact, under
# orthographic projection the whole translation/orientation thing
# can be scrapped for the detector. XXX look up include,
# include_scope for phil XXX Hardcoded address for now.
address = "CxiDs1-0|Cspad-0"
metrology_str = "detector { serial = %d\n" % 0
metrology_str += "label = %s\n" % address
# The center of the detector is defined as the average of all the
# sections it contains. The first coordinate of the matrix-oriented
# coordinate system of the Section class maps to -y, the second to
# x, and the third to z. While the detector still sits on the
# origin (zero translation), the mapping from the origin in Section
# coordinates is still needed.
t_d = [0, 0, 0]
nmemb = 0
for p in xrange(len(sections)):
for s in xrange(len(sections[p])):
t_d[0] += +sections[p][s].center[1]
t_d[1] += -sections[p][s].center[0]
t_d[2] += 0
nmemb += 1
if (nmemb > 0):
for i in xrange(3):
t_d[i] /= nmemb
metrology_str += "translation = 0, 0, 0\n"
o_d = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=0, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in o_d)
for p in xrange(len(sections)):
# Loop over quadrants (panels). XXX Translation of panels is
# wrongly set to to centre of sections in the quadrant
# w.r.t. center of the detector.
metrology_str += "panel { serial = %d\n" % p
metrology_str += "translation = "
t_p = [0, 0, 0]
for s in xrange(len(sections[p])):
t_p[0] += +sections[p][s].center[1] - t_d[0]
t_p[1] += -sections[p][s].center[0] - t_d[1]
t_p[2] += 0 - t_d[2]
for i in xrange(3):
t_p[i] /= len(sections[p])
metrology_str += "%s" % repr(t_p[i] * pixel_size)
if (i < 2):
metrology_str += ", "
else:
metrology_str += "\n"
# XXX Orientation wrongly set to zero.
o_p = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=0, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in o_p)
for s in xrange(len(sections[p])):
# Loop over sensors (sections or two-by-one:s). Note that
# sensors are rotated by -90 degrees in the SLAC metrology
# convention w.r.t. their appearance in the XTC stream.
s_t = [0, 0, 0]
s_t[0] = +sections[p][s].center[1] - t_p[0] - t_d[0]
s_t[1] = -sections[p][s].center[0] - t_p[1] - t_d[1]
s_t[2] = 0 - t_p[2] - t_d[2]
metrology_str += "sensor { serial = %d\n" % s
metrology_str += "translation = "
for i in xrange(3):
metrology_str += "%s" % repr(s_t[i] * pixel_size)
if (i < 2):
metrology_str += ", "
else:
metrology_str += "\n"
s_o = matrix.col([0, 0, 1]).axis_and_angle_as_unit_quaternion(
angle=sections[p][s].angle - 90, deg=True)
metrology_str += "orientation = %s, %s, %s, %s\n" % \
tuple(repr(c) for c in s_o)
for a in xrange(2):
# The ASIC:s of the CSPad are 185 rows by 194 columns. The
# ASIC:s are horizontally aligned within a section, with a
# three-column gap between them.
metrology_str += "asic { serial = %d\n" % a
if (a == 0):
metrology_str += "translation = %s, %s, %s\n" % (
repr(-(194 + 3) / 2 * pixel_size), "0", "0") # XXX hardcoded!
else:
metrology_str += "translation = %s, %s, %s\n" % (
repr(+(194 + 3) / 2 * pixel_size), "0", "0") # XXX hardcoded!
metrology_str += "orientation = 1, 0, 0, 0\n"
metrology_str += "pixel_size = %s, %s\n" % (
repr(pixel_size), repr(pixel_size))
metrology_str += "dimension = %d, %d\n" % (194, 185) # XXX hardcoded!
metrology_str += "saturation = %s\n" % repr(float(saturated_value))
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_str += "}\n"
metrology_phil = master_phil.fetch(
sources=[phil.parse(metrology_str)])
return (metrology_phil)
def run(argv=None):
if (argv is None):
argv = sys.argv
# XXX Could/should handle effective metrology the same way, except
# it does not have a single scope.
work_phil = phil.process_command_line(
args=argv[1:],
master_string=master_str + phil_str + additional_spotfinder_phil_defs)
work_params = work_phil.work.extract()
app = wx.App(0)
wx.SystemOptions.SetOptionInt("osx.openfiledialog.always-show-types", 1)
frame = XrayFrame(None, -1, "X-ray image display", size=(800,720))
frame.Show()
# show settings panel
frame.OnShowSettings(None)
frame.settings_frame.panel.center_ctrl.SetValue(
work_params.beam_center)
frame.settings_frame.panel.integ_ctrl.SetValue(
work_params.show_integration_results)
frame.settings_frame.panel.spots_ctrl.SetValue(
work_params.show_spotfinder_results)
frame.settings.show_effective_tiling = work_params.show_effective_tiling
frame.settings_frame.panel.collect_values()
if (work_params.effective_metrology is not None):
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
stream = open(work_params.effective_metrology)
metrology_phil = master_phil.fetch(sources=[phil.parse(stream.read())])
stream.close()
frame.metrology_matrices = metrology_as_transformation_matrices(
metrology_phil.extract())
# Update initial settings with values from the command line. Needs
# to be done before image is loaded (but after the frame is
# instantiated).
frame.params = work_params
frame.init_pyslip()
frame.pyslip.tiles.user_requests_antialiasing = work_params.anti_aliasing
frame.pyslip.tiles.show_untrusted = frame.params.show_untrusted
paths = work_phil.remaining_args
if (len(paths) == 1 and os.path.basename(paths[0]) == "DISTL_pickle"):
assert os.path.isfile(paths[0])
frame.load_distl_output(paths[0])
elif (len(paths) > 0):
frame.CHOOSER_SIZE = 1500
from dxtbx.imageset import ImageSetFactory
from rstbx.slip_viewer.frame import chooser_wrapper
sets = ImageSetFactory.new(paths)
for imgset in sets:
for idx in imgset.indices():
frame.add_file_name_or_data(chooser_wrapper(imgset, idx))
idx = sets[0].indices()[0]
frame.load_image(chooser_wrapper(sets[0],idx))
app.MainLoop()
return 0
