def UpdateMagnification(self):
# Total magnification
mag = self._mpp_screen / self._microscope_view.mpp.value
label = u"Mag: × %s" % units.readable_str(
units.round_significant(mag, 3))
# Gather all different image mpp values
mpps = set()
for im, stream in self._microscope_view.stream_tree.getImages():
try:
if hasattr(stream, 'mpp'): # im is a tuple of tuple of tiles
mpps.add(stream.mpp.min)
else:
md = im.metadata
mpps.add(md[model.MD_PIXEL_SIZE][0])
except KeyError:
pass
# If there's only one mpp value (i.e. there's only one image, or they
# all have the same mpp value), indicate the digital zoom.
if len(mpps) == 1:
mpp_im = mpps.pop()
# mag_im = self._mpp_screen / mpp_im # as if 1 im.px == 1 sc.px
mag_dig = mpp_im / self._microscope_view.mpp.value
label += u" (Digital: × %s)" % units.readable_str(
units.round_significant(mag_dig, 2))
if self.bottom_legend:
self.bottom_legend.set_mag_label(label)
def acquire(comp_name, dataflow_names, filename):
"""
Acquire an image from one (or more) dataflow
comp_name (string): name of the detector to find
dataflow_names (list of string): name of each dataflow to access
filename (unicode): name of the output file (format depends on the extension)
"""
component = get_detector(comp_name)
# check the dataflow exists
dataflows = []
for df_name in dataflow_names:
try:
df = getattr(component, df_name)
except AttributeError:
raise ValueError("Failed to find data-flow '%s' on component %s" %
(df_name, comp_name))
if not isinstance(df, model.DataFlowBase):
raise ValueError("%s.%s is not a data-flow" % (comp_name, df_name))
dataflows.append(df)
images = []
for df in dataflows:
try:
# Note: currently, get() uses Pyro, which is not as memory efficient
# as .subscribe(), which uses ZMQ. So would need to use
# _get_big_image() if very large image is requested.
image = df.get()
except Exception as exc:
raise IOError("Failed to acquire image from component %s: %s" %
(comp_name, exc))
logging.info("Acquired an image of dimension %r.", image.shape)
images.append(image)
try:
if model.MD_PIXEL_SIZE in image.metadata:
pxs = image.metadata[model.MD_PIXEL_SIZE]
dim = (image.shape[0] * pxs[0], image.shape[1] * pxs[1])
logging.info("Physical dimension of image is %s.",
units.readable_str(dim, unit="m", sig=3))
else:
logging.warning("Physical dimension of image is unknown.")
if model.MD_SENSOR_PIXEL_SIZE in image.metadata:
spxs = image.metadata[model.MD_SENSOR_PIXEL_SIZE]
dim_sens = (image.shape[0] * spxs[0], image.shape[1] * spxs[1])
logging.info("Physical dimension of sensor is %s.",
units.readable_str(dim_sens, unit="m", sig=3))
except Exception as exc:
logging.exception("Failed to read image information.")
exporter = dataio.find_fittest_converter(filename)
try:
exporter.export(filename, images)
except IOError as exc:
raise IOError(u"Failed to save to '%s': %s" % (filename, exc))
def acquire(comp_name, dataflow_names, filename):
"""
Acquire an image from one (or more) dataflow
comp_name (string): name of the detector to find
dataflow_names (list of string): name of each dataflow to access
filename (unicode): name of the output file (format depends on the extension)
"""
component = get_detector(comp_name)
# check the dataflow exists
dataflows = []
for df_name in dataflow_names:
try:
df = getattr(component, df_name)
except AttributeError:
raise ValueError("Failed to find data-flow '%s' on component %s" % (df_name, comp_name))
if not isinstance(df, model.DataFlowBase):
raise ValueError("%s.%s is not a data-flow" % (comp_name, df_name))
dataflows.append(df)
images = []
for df in dataflows:
try:
# Note: currently, get() uses Pyro, which is not as memory efficient
# as .subscribe(), which uses ZMQ. So would need to use
# _get_big_image() if very large image is requested.
image = df.get()
except Exception as exc:
raise IOError("Failed to acquire image from component %s: %s" % (comp_name, exc))
logging.info("Acquired an image of dimension %r.", image.shape)
images.append(image)
try:
if model.MD_PIXEL_SIZE in image.metadata:
pxs = image.metadata[model.MD_PIXEL_SIZE]
dim = (image.shape[0] * pxs[0], image.shape[1] * pxs[1])
logging.info("Physical dimension of image is %s.",
units.readable_str(dim, unit="m", sig=3))
else:
logging.warning("Physical dimension of image is unknown.")
if model.MD_SENSOR_PIXEL_SIZE in image.metadata:
spxs = image.metadata[model.MD_SENSOR_PIXEL_SIZE]
dim_sens = (image.shape[0] * spxs[0], image.shape[1] * spxs[1])
logging.info("Physical dimension of sensor is %s.",
units.readable_str(dim_sens, unit="m", sig=3))
except Exception as exc:
logging.exception("Failed to read image information.")
exporter = dataio.find_fittest_converter(filename)
try:
exporter.export(filename, images)
except IOError as exc:
raise IOError(u"Failed to save to '%s': %s" % (filename, exc))
def draw(self, ctx):
# TODO: Both focuses at the same time, or 'snap' to horizontal/vertical on first motion?
ctx.set_line_width(10)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(1.0, 1.0, 1.0, 0.8)
x, y = self.cnvs.ClientSize
# Horizontal
if self.shifts[0] is not None:
y -= self.margin + (self.line_width // 2)
middle = x / 2
# don't display extremely small values, which are due to accumulation
# of floating point error
shiftm = self.shifts[0]
if abs(shiftm) < 1e-12:
shiftm = 0
shift = shiftm * self.ppm[0]
end_x = middle + (middle * (shift / (x / 2)))
end_x = min(max(self.margin, end_x), x - self.margin)
ctx.move_to(middle, y)
ctx.line_to(end_x, y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(shiftm, "m", 2)
self.focus_label.text = lbl
self.focus_label.pos = (end_x, y - 15)
self._write_label(ctx, self.focus_label)
# Vertical
if self.shifts[1] is not None:
x -= self.margin + (self.line_width // 2)
middle = y / 2
# don't display extremely small values, which are due to accumulation
# of floating point error
shiftm = self.shifts[1]
if abs(shiftm) < 1e-12:
shiftm = 0
shift = shiftm * self.ppm[1]
end_y = middle - (middle * (shift / (y / 2)))
end_y = min(max(self.margin, end_y), y - self.margin)
ctx.move_to(x, middle)
ctx.line_to(x, end_y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(shiftm, "m", 2)
self.focus_label.text = lbl
self.focus_label.pos = (x - 15, end_y)
self._write_label(ctx, self.focus_label)
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
self._acq_future = None # To avoid holding the ref in memory
self._faf_connector = None
try:
trans_val, cor_md = future.result()
opt_md, sem_md = cor_md
# Save the optical correction metadata straight into the CCD
main_data.ccd.updateMetadata(opt_md)
# The SEM correction metadata goes to the ebeam
main_data.ebeam.updateMetadata(sem_md)
except CancelledError:
self._tab_panel.lbl_fine_align.Label = "Cancelled"
except Exception:
self._tab_panel.lbl_fine_align.Label = "Failed"
else:
self._tab_panel.lbl_fine_align.Label = "Successful"
self._main_frame.menu_item_reset_finealign.Enable(True)
# Temporary info until the GUI can actually rotate the images
rot = math.degrees(opt_md.get(model.MD_ROTATION_COR, 0))
shear = sem_md.get(model.MD_SHEAR_COR, 0)
scaling_xy = sem_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))
# the worse is the rotation, the longer it's displayed
timeout = max(2, min(abs(rot), 10))
popup.show_message(
self._tab_panel,
u"Rotation applied: %s\nShear applied: %s\nX/Y Scaling applied: %s"
% (units.readable_str(rot, unit="°", sig=3),
units.readable_str(shear, sig=3),
units.readable_str(scaling_xy, sig=3)),
timeout=timeout
)
logging.warning("Fine alignment computed rotation needed of %f°, "
"shear needed of %s, and X/Y scaling needed of %s.",
rot, shear, scaling_xy)
# As the CCD image might have different pixel size, force to fit
self._tab_panel.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._tab_panel.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_fine_align)
self._tab_panel.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._tab_panel.lbl_fine_align.Show()
self._tab_panel.gauge_fine_align.Hide()
self._sizer.Layout()
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
self._acq_future = None # To avoid holding the ref in memory
self._faf_connector = None
try:
trans_val, cor_md = future.result()
opt_md, sem_md = cor_md
# Save the optical correction metadata straight into the CCD
main_data.ccd.updateMetadata(opt_md)
# The SEM correction metadata goes to the ebeam
main_data.ebeam.updateMetadata(sem_md)
except CancelledError:
self._tab_panel.lbl_fine_align.Label = "Cancelled"
except Exception:
self._tab_panel.lbl_fine_align.Label = "Failed"
else:
self._tab_panel.lbl_fine_align.Label = "Successful"
self._main_frame.menu_item_reset_finealign.Enable(True)
# Temporary info until the GUI can actually rotate the images
rot = math.degrees(opt_md.get(model.MD_ROTATION_COR, 0))
shear = sem_md.get(model.MD_SHEAR_COR, 0)
scaling_xy = sem_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))
# the worse is the rotation, the longer it's displayed
timeout = max(2, min(abs(rot), 10))
popup.show_message(
self._tab_panel,
u"Rotation applied: %s\nShear applied: %s\nX/Y Scaling applied: %s"
% (units.readable_str(
rot, unit="°", sig=3), units.readable_str(
shear, sig=3), units.readable_str(scaling_xy, sig=3)),
timeout=timeout)
logging.warning(
"Fine alignment computed rotation needed of %f°, "
"shear needed of %s, and X/Y scaling needed of %s.", rot,
shear, scaling_xy)
# As the CCD image might have different pixel size, force to fit
self._tab_panel.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._tab_panel.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_fine_align)
self._tab_panel.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._tab_panel.lbl_fine_align.Show()
self._tab_panel.gauge_fine_align.Hide()
self._sizer.Layout()
def test_readable_str(self):
# (input) (expected output)
values = [
((1.0, None), "1"),
((1, None), "1"),
((-1.234, "m"), "-1.234 m"),
((-1234, "g"), "-1.234 kg"),
((160000, None), "160000"),
((16, None), "16"),
((160001, None, 3), "160000"),
((16000000.0, None), "16000000"),
((16.3000000001, "px", 3), "16.3 px"),
((numpy.float64(16.3), "px", 3), "16.3 px"),
((-1600, "N"), "-1.6 kN"),
((-1601, "N", 3), "-1.6 kN"), # sig=3
((0.0001236, None), "0.0001236"),
((0.0012, "V"), "1.2 mV"),
((999.999, "V", 3), "1 kV"),
((999.5, "V"), "999.5 V"),
((999.5, "V", 3), "1 kV"),
((999.4, "V", 3), "999 V"),
((200e-6, "m"), u"200 µm"),
((0.0, "m"), "0 m"),
(([1500, 1200, 150], None), "1500 x 1200 x 150"),
(([0.0001236, 0.00014], "m"), u"123.6 x 140 µm"),
(([0.0001236, 12.0], "m"), "0.0001236 x 12 m"),
(([1200,
1000], "px"), "1200 x 1000 px"), # special non-prefix unit
(([-float("inf"), float("NaN")], "m"), u"-∞ x unknown m"),
]
for (i, eo) in values:
o = units.readable_str(*i)
self.assertEqual(o, eo,
u"%s is '%s' while expected '%s'" % (i, o, eo))
def test_readable_str(self):
# (input) (expected output)
values = [((1.0, None), "1"),
((1, None), "1"),
((-1.234, "m"), "-1.234 m"),
((-1234, "g"), "-1.234 kg"),
((160000, None), "160000"),
((16L, None), "16"),
((160001, None, 3), "160000"),
((16000000.0, None), "16000000"),
((-1600, "N"), "-1.6 kN"),
((-1601, "N", 3), "-1.6 kN"), # sig=3
((0.0001236, None), "0.0001236"),
((0.0012, "V"), "1.2 mV"),
((200e-6, "m"), u"200 µm"),
((0.0, "m"), "0 m"),
(([1500, 1200, 150], None), "1500 x 1200 x 150"),
(([0.0001236, 0.00014], "m"), u"123.6 x 140 µm"),
(([0.0001236, 12.0], "m"), "0.0001236 x 12 m"),
(([1200, 1000], "px"), "1200 x 1000 px"), # special non-prefix unit
(([-float("inf"), float("NaN")], "m"), u"-∞ x unknown m"),
]
for (i, eo) in values:
o = units.readable_str(*i)
self.assertEquals(o, eo,
u"%s is '%s' while expected '%s'" % (i, o, eo))
def Draw(self, ctx):
"""
Draws the crosshair
dc (wx.DC)
"""
# TODO: handle displaying the focus 0 (horizontally)
if self.shifts[1]:
ctx.set_line_width(10)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(1.0, 1.0, 1.0, 0.8)
x, y = self.cnvs.ClientSize
x -= self.margin + (self.line_width // 2)
middle = y / 2
shift = self.shifts[1] * 1e6 # typically within µm
end_y = middle - (middle * (shift / (y / 2)))
end_y = min(max(self.margin, end_y), y - self.margin)
ctx.move_to(x, middle)
ctx.line_to(x, end_y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[1], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (x - 15, end_y)
self._write_label(ctx, self.focus_label)
def _display_pretty(self):
if self._number_value is None:
str_val = u""
elif self._number_value == 0 and self.unit not in units.IGNORE_UNITS:
# Special case with 0: readable_str return just "0 unit", without
# prefix. This is technically correct, but quite inconvenient and
# a little strange when the typical value has a prefix (eg, nm, kV).
# => use prefix of key_step (as it's a "small value")
if self.key_step:
_, prefix = units.get_si_scale(self.key_step)
elif self.key_step_min:
_, prefix = units.get_si_scale(self.key_step_min)
else:
prefix = ""
str_val = "0 %s%s" % (prefix, self.unit)
else:
str_val = units.readable_str(self._number_value, self.unit,
self.accuracy)
# Get the length of the number, without the unit (number and unit are separated by a space)
number_length = str_val.find(" ")
if number_length < 0: # No space found -> only numbers
number_length = len(str_val)
wx.TextCtrl.ChangeValue(self, str_val)
# Select the number value
wx.CallAfter(self.SetSelection, number_length, number_length)
def add_metadata(self, key, value):
""" Adds an entry representing specific metadata
According to the metadata key, the right representation is used for the value.
:param key: (model.MD_*) the metadata key
:param value: (depends on the metadata) the value to display
"""
# By default the key is a nice user-readable string
label = str(key)
# Convert value to a nice string according to the metadata type
try:
if key == model.MD_ACQ_DATE:
# convert to a date using the user's preferences
nice_str = time.strftime("%c", time.localtime(value))
# In Python 2, we still need to convert it to unicode
if isinstance(nice_str, bytes):
nice_str = nice_str.decode(locale.getpreferredencoding())
else:
# Still try to beautify a bit if it's a number
if (isinstance(value, (int, long, float)) or
(isinstance(value, collections.Iterable) and len(value) > 0
and isinstance(value[0], (int, long, float)))):
nice_str = readable_str(value, sig=3)
else:
nice_str = str(value)
except Exception:
logging.exception("Trying to convert metadata %s", key)
nice_str = "N/A"
self.panel.add_readonly_field(label, nice_str)
def Draw(self, ctx):
"""
Draws the crosshair
dc (wx.DC)
"""
# TODO: handle displaying the focus 0 (horizontally)
if self.shifts[1]:
ctx.set_line_width(10)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(1.0, 1.0, 1.0, 0.8)
x, y = self.cnvs.ClientSize
x -= self.margin + (self.line_width // 2)
middle = y / 2
shift = self.shifts[1] * 1e6 # typically within µm
end_y = middle - (middle * (shift / (y / 2)))
end_y = min(max(self.margin, end_y), y - self.margin)
ctx.move_to(x, middle)
ctx.line_to(x, end_y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[1], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (x - 15, end_y)
self._write_label(ctx, self.focus_label)
def add_metadata(self, key, value):
""" Adds an entry representing specific metadata
According to the metadata key, the right representation is used for the value.
:param key: (model.MD_*) the metadata key
:param value: (depends on the metadata) the value to display
"""
# By default the key is a nice user-readable string
label = unicode(key)
# Convert value to a nice string according to the metadata type
try:
if key == model.MD_ACQ_DATE:
# convert to a date using the user's preferences
nice_str = time.strftime(u"%c", time.localtime(value))
else:
# Still try to beautify a bit if it's a number
if isinstance(value, (int, long, float)) or (
isinstance(value, collections.Iterable)
and len(value) > 0
and isinstance(value[0], (int, long, float))
):
nice_str = readable_str(value, sig=3)
else:
nice_str = unicode(value)
except Exception:
logging.exception("Trying to convert metadata %s", key)
nice_str = "N/A"
self.panel.add_readonly_field(label, nice_str)
def Draw(self, ctx, shift=(0, 0), scale=1.0):
if self.w_start_pos and self.w_end_pos:
ctx.save()
# Important: We need to use the world positions, in order to draw everything at the
# right scale.
offset = self.cnvs.get_half_buffer_size()
b_pos = (self.cnvs.world_to_buffer(self.w_start_pos, offset) +
self.cnvs.world_to_buffer(self.w_end_pos, offset))
b_pos = self._normalize(b_pos)
self.update_from_buffer(b_pos[:2], b_pos[2:4], shift + (scale, ))
#logging.warn("%s %s", shift, world_to_buffer_pos(shift))
rect = (b_pos[0] + 0.5, b_pos[1] + 0.5, b_pos[2] - b_pos[0],
b_pos[3] - b_pos[1])
# draws a light black background for the rectangle
ctx.set_line_width(4)
ctx.set_source_rgba(0, 0, 0, 0.5)
ctx.rectangle(*rect)
ctx.stroke()
# draws the dotted line
ctx.set_line_width(2)
ctx.set_dash([3])
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(*self.colour)
ctx.rectangle(*rect)
ctx.stroke()
# Label
if (self.selection_mode
in (base.SEL_MODE_EDIT, base.SEL_MODE_CREATE)
and self.cnvs.microscope_view):
w, h = self.cnvs.selection_to_real_size(
self.w_start_pos, self.w_end_pos)
w = units.readable_str(w, 'm', sig=2)
h = units.readable_str(h, 'm', sig=2)
size_lbl = u"{} x {}".format(w, h)
pos = (b_pos[2] + 8, b_pos[3] - 10)
self.position_label.pos = pos
self.position_label.text = size_lbl
self._write_labels(ctx)
ctx.restore()
def format_axis_choices(name, axis_def):
"""
Transform the given choices for an axis into an user friendly display
name (str): the name of the axis
axis_def (Axis): the axis definition
returns:
choices_formatted (None or list of (value, str): axis value/user-friendly
display name (including the unit). None if axis doesn't support choices.
"""
try:
choices = axis_def.choices
except AttributeError:
return None
if not choices:
return None
unit = axis_def.unit
if isinstance(choices, dict):
choices_formatted = list(choices.items())
# In this case, normally the values are already formatted, but for
# wavelength band, the "formatted" value is still a band info (ie, two
# values in m)
if name == "band":
def to_readable_band(v):
if (isinstance(v, (tuple, list)) and len(v) > 1 and
all(isinstance(c, numbers.Real) for c in v)):
return fluo.to_readable_band(v)
else:
return v
choices_formatted = [(k, to_readable_band(v)) for k, v in choices_formatted]
elif len(choices) > 1 and all(isinstance(c, numbers.Real) for c in choices):
choices_formatted = None
try:
choices = sorted(choices)
# Can we fit them (more or less) all with the same unit prefix?
mn_non0 = min(c for c in choices if c != 0)
if abs(choices[-1] / mn_non0) < 1000:
fmt, choices_si_prefix = utun.si_scale_list(choices)
fmt = [utun.to_string_pretty(c, 3, unit) for c in fmt]
choices_formatted = list(zip(choices, fmt))
except Exception:
logging.exception("Formatting error for %s", choices)
if choices_formatted is None:
choices_formatted = [(c, readable_str(c, unit=unit, sig=3)) for c in choices]
else:
choices_formatted = [(c, u"%s %s" % (choice_to_str(c), unit)) for c in choices]
if not isinstance(choices, OrderedDict):
# sort 2-tuples = according to first value in tuple
choices_formatted = sorted(choices_formatted)
return choices_formatted
def format_axis_choices(name, axis_def):
"""
Transform the given choices for an axis into an user friendly display
name (str): the name of the axis
axis_def (Axis): the axis definition
returns:
choices_formatted (None or list of (value, str): axis value/user-friendly
display name (including the unit). None if axis doesn't support choices.
"""
try:
choices = axis_def.choices
except AttributeError:
return None
if not choices:
return None
unit = axis_def.unit
if isinstance(choices, dict):
choices_formatted = choices.items()
# In this case, normally the values are already formatted, but for
# wavelength band, the "formatted" value is still a band info (ie, two
# values in m)
if name == "band":
def to_readable_band(v):
if (isinstance(v, (tuple, list)) and len(v) > 1 and
all(isinstance(c, numbers.Real) for c in v)):
return fluo.to_readable_band(v)
else:
return v
choices_formatted = [(k, to_readable_band(v)) for k, v in choices_formatted]
elif len(choices) > 1 and all(isinstance(c, numbers.Real) for c in choices):
choices_formatted = None
try:
choices = sorted(choices)
# Can we fit them (more or less) all with the same unit prefix?
mn_non0 = min(c for c in choices if c != 0)
if abs(choices[-1] / mn_non0) < 1000:
fmt, choices_si_prefix = utun.si_scale_list(choices)
fmt = [utun.to_string_pretty(c, 3, unit) for c in fmt]
choices_formatted = zip(choices, fmt)
except Exception:
logging.exception("Formatting error for %s", choices)
if choices_formatted is None:
choices_formatted = [(c, readable_str(c, unit=unit, sig=3)) for c in choices]
else:
choices_formatted = [(c, u"%s %s" % (choice_to_str(c), unit)) for c in choices]
if not isinstance(choices, OrderedDict):
# sort 2-tuples = according to first value in tuple
choices_formatted = sorted(choices_formatted)
return choices_formatted
def move(comp_name, moves, check_distance=True, to_radians=False):
"""
move (relatively) the axis of the given component by the specified amount of µm
comp_name (str): name of the component
moves (dict str -> str): axis -> distance (as text, and in µm for distances)
check_distance (bool): if the axis is in meters, check that the move is not
too big.
to_radians (bool): will convert from degrees to radians if the axis is in radians,
otherwise will fail
"""
# for safety reason, we use µm instead of meters, as it's harder to type a
# huge distance
component = get_component(comp_name)
act_mv = {} # axis -> value
for axis_name, str_distance in moves.items():
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
# Use convert_to_object() to allow typing negative values with e:
# -1e-6 => '!!float -1.0e-6'. It's not very nice, but does work.
distance = float(convert_to_object(str_distance)) * 1e-6 # µm -> m
except ValueError:
raise ValueError("Distance '%s' cannot be converted to a number" %
str_distance)
if check_distance and abs(distance) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m), use '--big-distance' to allow the move." %
(abs(distance), MAX_DISTANCE))
else:
distance = convert_to_object(str_distance)
if to_radians:
if ad.unit == "rad":
distance = math.radians(distance)
else:
raise ValueError("Axis %s is in %s, doesn't support value in degrees" % (axis_name, ad.unit))
act_mv[axis_name] = distance
logging.info(u"Will move %s.%s by %s", comp_name, axis_name,
units.readable_str(distance, ad.unit, sig=3))
try:
m = component.moveRel(act_mv)
try:
m.result(120)
except KeyboardInterrupt:
logging.warning("Cancelling relative move of component %s", comp_name)
m.cancel()
raise
except Exception as exc:
raise IOError("Failed to move component %s by %s: %s" %
(comp_name, act_mv, exc))
def UpdateHFWLabel(self):
""" Physical width of the display"""
if not self._microscope_view:
return
hfw = self._microscope_view.mpp.value * self.GetClientSize()[0]
hfw = units.round_significant(hfw, 4)
label = u"HFW: %s" % units.readable_str(hfw, "m", sig=3)
self.bottom_legend.set_hfw_label(label)
def _update_label(self, pressure_val):
""" Set a formatted pressure value as the label of the button """
str_value = units.readable_str(
pressure_val, sig=2, unit=self.main_data.chamber.pressure.unit)
if self.btn.Label != str_value:
self.btn.Label = str_value
self.btn.Refresh()
def Draw(self, ctx, shift=(0, 0), scale=1.0):
if self.w_start_pos and self.w_end_pos:
ctx.save()
# Important: We need to use the world positions, in order to draw everything at the
# right scale.
offset = self.cnvs.get_half_buffer_size()
b_pos = (self.cnvs.world_to_buffer(self.w_start_pos, offset) +
self.cnvs.world_to_buffer(self.w_end_pos, offset))
b_pos = self._normalize(b_pos)
self.update_from_buffer(b_pos[:2], b_pos[2:4], shift + (scale,))
#logging.warn("%s %s", shift, world_to_buffer_pos(shift))
rect = (b_pos[0] + 0.5, b_pos[1] + 0.5,
b_pos[2] - b_pos[0], b_pos[3] - b_pos[1])
# draws a light black background for the rectangle
ctx.set_line_width(4)
ctx.set_source_rgba(0, 0, 0, 0.5)
ctx.rectangle(*rect)
ctx.stroke()
# draws the dotted line
ctx.set_line_width(2)
ctx.set_dash([3])
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(*self.colour)
ctx.rectangle(*rect)
ctx.stroke()
# Label
if (self.selection_mode in (base.SEL_MODE_EDIT, base.SEL_MODE_CREATE) and
self.cnvs.microscope_view):
w, h = self.cnvs.selection_to_real_size(self.w_start_pos, self.w_end_pos)
w = units.readable_str(w, 'm', sig=2)
h = units.readable_str(h, 'm', sig=2)
size_lbl = u"{} x {}".format(w, h)
pos = (b_pos[2] + 8, b_pos[3] - 10)
self.position_label.pos = pos
self.position_label.text = size_lbl
self._write_labels(ctx)
ctx.restore()
def Draw(self, ctx):
# TODO: Both focuses at the same time, or 'snap' to horizontal/vertical on first motion?
ctx.set_line_width(10)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(1.0, 1.0, 1.0, 0.8)
x, y = self.cnvs.ClientSize
# Horizontal
if self.shifts[0]:
y -= self.margin + (self.line_width // 2)
middle = x / 2
shift = self.shifts[0] * 1e6 # typically within µm
end_x = middle + (middle * (shift / (x / 2)))
end_x = min(max(self.margin, end_x), x - self.margin)
ctx.move_to(middle, y)
ctx.line_to(end_x, y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[0], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (end_x, y - 15)
self._write_label(ctx, self.focus_label)
# Vertical
if self.shifts[1]:
x -= self.margin + (self.line_width // 2)
middle = y / 2
shift = self.shifts[1] * 1e6 # typically within µm
end_y = middle - (middle * (shift / (y / 2)))
end_y = min(max(self.margin, end_y), y - self.margin)
ctx.move_to(x, middle)
ctx.line_to(x, end_y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[1], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (x - 15, end_y)
self._write_label(ctx, self.focus_label)
def Draw(self, ctx):
# TODO: Both focuses at the same time, or 'snap' to horizontal/vertical on first motion?
ctx.set_line_width(10)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(1.0, 1.0, 1.0, 0.8)
x, y = self.cnvs.ClientSize
# Horizontal
if self.shifts[0]:
y -= self.margin + (self.line_width // 2)
middle = x / 2
shift = self.shifts[0] * 1e6 # typically within µm
end_x = middle + (middle * (shift / (x / 2)))
end_x = min(max(self.margin, end_x), x - self.margin)
ctx.move_to(middle, y)
ctx.line_to(end_x, y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[0], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (end_x, y - 15)
self._write_label(ctx, self.focus_label)
# Vertical
if self.shifts[1]:
x -= self.margin + (self.line_width // 2)
middle = y / 2
shift = self.shifts[1] * 1e6 # typically within µm
end_y = middle - (middle * (shift / (y / 2)))
end_y = min(max(self.margin, end_y), y - self.margin)
ctx.move_to(x, middle)
ctx.line_to(x, end_y)
ctx.stroke()
lbl = "focus %s" % units.readable_str(self.shifts[1], 'm', 2)
self.focus_label.text = lbl
self.focus_label.pos = (x - 15, end_y)
self._write_label(ctx, self.focus_label)
def on_paint(self, _):
if self._value_range is None:
return
# shared function with the export method
self._tick_list, self._vtp_ratio = calculate_ticks(
self._value_range, self.ClientSize, self._orientation,
self._tick_spacing)
csize = self.ClientSize
# Set Font
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
max_width = 0
prev_lpos = 0 if self._orientation == wx.HORIZONTAL else csize.y
for i, (pos, val) in enumerate(self._tick_list):
label = units.readable_str(val, self.unit, 3)
_, _, lbl_width, lbl_height, _, _ = ctx.text_extents(label)
if self._orientation == wx.HORIZONTAL:
lpos = pos - (lbl_width // 2)
lpos = max(min(lpos, csize.x - lbl_width - 2), 2)
# print (i, prev_right, lpos)
if prev_lpos < lpos:
ctx.move_to(lpos, lbl_height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
prev_lpos = lpos + lbl_width
else:
max_width = max(max_width, lbl_width)
lpos = pos + (lbl_height // 2)
lpos = max(min(lpos, csize.y), 2)
if prev_lpos >= lpos + 20 or i == 0:
ctx.move_to(csize.x - lbl_width - 9, lpos)
ctx.show_text(label)
ctx.move_to(csize.x - 5, pos)
ctx.line_to(csize.x, pos)
prev_lpos = lpos + lbl_height
ctx.stroke()
if self._orientation == wx.VERTICAL and max_width != self._max_tick_width:
self._max_tick_width = max_width
self.SetMinSize((self._max_tick_width + 14, -1))
self.Parent.GetSizer().Layout()
def Draw(self, ctx, shift=(0, 0), scale=1.0):
if self.w_start_pos and self.w_end_pos:
offset = [v // 2 for v in self.cnvs._bmp_buffer_size]
b_pos = (self.cnvs.world_to_buffer(self.w_start_pos, offset) +
self.cnvs.world_to_buffer(self.w_end_pos, offset))
b_pos = util.normalize_rect(b_pos)
self.update_from_buffer(b_pos[:2], b_pos[2:4], shift + (scale,))
#logging.warn("%s %s", shift, world_to_buffer_pos(shift))
rect = (b_pos[0] + 0.5, b_pos[1] + 0.5,
b_pos[2] - b_pos[0], b_pos[3] - b_pos[1])
# draws a light black background for the rectangle
ctx.set_line_width(2.5)
ctx.set_source_rgba(0, 0, 0, 0.5)
ctx.rectangle(*rect)
ctx.stroke()
# draws the dotted line
ctx.set_line_width(2)
ctx.set_dash([3,])
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(*self.colour)
ctx.rectangle(*rect)
ctx.stroke()
# Label
if (self.dragging or self.edit) and self.cnvs.microscope_view:
w, h = self.cnvs.selection_to_real_size(
self.w_start_pos,
self.w_end_pos
)
w = units.readable_str(w, 'm', sig=2)
h = units.readable_str(h, 'm', sig=2)
size_lbl = u"{} x {}".format(w, h)
pos = (b_pos[2] + 10, b_pos[3] + 5)
self.position_label.pos = pos
self.position_label.text = size_lbl
self._write_labels(ctx)
def _display_pretty(self):
if self._number_value is None:
str_val = u""
else:
str_val = units.readable_str(self._number_value, self.unit, self.accuracy)
# Get the length of the number (string length, minus the unit length)
number_length = len(str_val.rstrip(string.ascii_letters + u" µ"))
wx.TextCtrl.ChangeValue(self, str_val)
# Select the number value
wx.CallAfter(self.SetSelection, number_length, number_length)
def draw(self, ctx):
ctx.set_line_width(self.line_width)
ctx.set_dash([3])
ctx.set_line_join(cairo.LINE_JOIN_MITER)
ctx.set_source_rgba(*self.colour)
if self.val.value is not None:
val = self.val.value
if self.map_y_from_x:
# Maps Y and also snap X to the closest X value in the data
val = self.cnvs.val_x_to_val(val[0])
v_pos = self.cnvs.val_to_pos(val)
self.x_label = units.readable_str(val[0], self.cnvs.unit_x, 3)
self.y_label = units.readable_str(val[1], self.cnvs.unit_y, 3)
# v_posx, v_posy = self.v_pos.value
if self.orientation & self.VERTICAL:
ctx.move_to(v_pos[0], 0)
ctx.line_to(v_pos[0], self.cnvs.ClientSize.y)
ctx.stroke()
if self.orientation & self.HORIZONTAL:
ctx.move_to(0, v_pos[1])
ctx.line_to(self.cnvs.ClientSize.x, v_pos[1])
ctx.stroke()
if self.x_label.text:
self.x_label.pos = (v_pos[0] + 5, self.cnvs.ClientSize.y)
self._write_label(ctx, self.x_label)
if self.y_label.text:
yp = max(0, v_pos[1] - 5) # Padding from line
# Increase bottom margin if x label is close
label_padding = 30 if v_pos[0] < 50 else 0
yn = min(self.view_height - label_padding, yp)
self.y_label.pos = (2, yn)
self._write_label(ctx, self.y_label)
r, g, b, a = conversion.change_brightness(self.colour, -0.2)
ctx.set_source_rgba(r, g, b, 0.5)
ctx.arc(v_pos[0], v_pos[1], 5.5, 0, 2 * math.pi)
ctx.fill()
def on_paint(self, _):
if self._value_range is None:
return
# shared function with the export method
self._tick_list, self._vtp_ratio = calculate_ticks(self._value_range, self.ClientSize, self._orientation, self._tick_spacing)
csize = self.ClientSize
# Set Font
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
max_width = 0
prev_lpos = 0 if self._orientation == wx.HORIZONTAL else csize.y
for i, (pos, val) in enumerate(self._tick_list):
label = units.readable_str(val, self.unit, 3)
_, _, lbl_width, lbl_height, _, _ = ctx.text_extents(label)
if self._orientation == wx.HORIZONTAL:
lpos = pos - (lbl_width // 2)
lpos = max(min(lpos, csize.x - lbl_width - 2), 2)
# print (i, prev_right, lpos)
if prev_lpos < lpos:
ctx.move_to(lpos, lbl_height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
prev_lpos = lpos + lbl_width
else:
max_width = max(max_width, lbl_width)
lpos = pos + (lbl_height // 2)
lpos = max(min(lpos, csize.y), 2)
if prev_lpos >= lpos + 20 or i == 0:
ctx.move_to(csize.x - lbl_width - 9, lpos)
ctx.show_text(label)
ctx.move_to(csize.x - 5, pos)
ctx.line_to(csize.x, pos)
prev_lpos = lpos + lbl_height
ctx.stroke()
if self._orientation == wx.VERTICAL and max_width != self._max_tick_width:
self._max_tick_width = max_width
self.SetMinSize((self._max_tick_width + 14, -1))
self.Parent.GetSizer().Layout()
def cb_set(value, ctrl=value_ctrl, u=unit):
for i in range(ctrl.Count):
if ctrl.GetClientData(i) == value:
logging.debug("Setting combobox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.debug("No existing label found for value %s in combobox ctrl %d",
value, id(ctrl))
# entering value as free text
txt = readable_str(value, u, sig=accuracy)
return ctrl.SetValue(txt)
def cb_set(value, ctrl=value_ctrl, unit=unit):
for i in range(ctrl.Count):
if ((isinstance(value, float) and util.almost_equal(ctrl.GetClientData(i), value)) or
ctrl.GetClientData(i) == value):
logging.debug("Setting ComboBox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.warning("No existing label found for value %s", value)
# entering value as free text
txt = readable_str(value, unit)
ctrl.SetValue(txt)
def on_paint(self, evt=None):
if not hasattr(self.Parent.canvas,
'has_data') or not self.Parent.canvas.has_data():
self.clear()
return
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
# TODO: only put label for some of the ticks
if not self.ticks:
self.calc_ticks(ctx)
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
max_width = 0
for i, (pos, val) in enumerate(self.ticks):
label = units.readable_str(val, self.unit, 3)
_, _, lbl_width, lbl_height, _, _ = ctx.text_extents(label)
if self.orientation == wx.HORIZONTAL:
lpos = pos - (lbl_width / 2)
lpos = max(min(lpos, self.ClientSize.x - lbl_width - 2), 2)
ctx.move_to(lpos, lbl_height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
else:
max_width = max(max_width, lbl_width)
lpos = pos + (lbl_height / 2)
lpos = max(min(lpos, self.ClientSize.y), 2)
ctx.move_to(self.ClientSize.x - lbl_width - 9, lpos)
ctx.show_text(label)
ctx.move_to(self.ClientSize.x - 5, pos)
ctx.line_to(self.ClientSize.x, pos)
ctx.stroke()
if self.orientation == wx.VERTICAL and max_width != self.max_tick_width:
self.max_tick_width = max_width
self.SetMinSize((self.max_tick_width + 14, -1))
self.Parent.GetSizer().Layout()
def UpdateMagnification(self):
# Total magnification
mag = self._mpp_screen / self._microscope_view.mpp.value
label = u"Mag: × %s" % units.readable_str(units.round_significant(mag, 3))
# Gather all different image mpp values
mpps = set()
for im in self._microscope_view.stream_tree.getImages():
try:
mpps.add(im.metadata[model.MD_PIXEL_SIZE][0])
except KeyError:
pass
# If there's only one mpp value (i.e. there's only one image, or they
# all have the same mpp value), indicate the digital zoom.
if len(mpps) == 1:
mpp_im = mpps.pop()
# mag_im = self._mpp_screen / mpp_im # as if 1 im.px == 1 sc.px
mag_dig = mpp_im / self._microscope_view.mpp.value
label += u" (Digital: × %s)" % units.readable_str(units.round_significant(mag_dig, 2))
self.bottom_legend.set_mag_label(label)
def move(comp_name, moves, check_distance=True):
"""
move (relatively) the axis of the given component by the specified amount of µm
comp_name (str): name of the component
check_distance (bool): if the axis is in meters, check that the move is not
too big.
moves (dict str -> str): axis -> distance (as text, and in µm for distances)
"""
# for safety reason, we use µm instead of meters, as it's harder to type a
# huge distance
component = get_component(comp_name)
act_mv = {} # axis -> value
for axis_name, str_distance in moves.items():
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
# Use convert_to_object() to allow typing negative values with e:
# -1e-6 => '!!float -1.0e-6'. It's not very nice, but does work.
distance = float(convert_to_object(str_distance)) * 1e-6 # µm -> m
except ValueError:
raise ValueError("Distance '%s' cannot be converted to a number" %
str_distance)
if check_distance and abs(distance) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m), use '--big-distance' to allow the move." %
(abs(distance), MAX_DISTANCE))
else:
distance = convert_to_object(str_distance)
act_mv[axis_name] = distance
logging.info(u"Will move %s.%s by %s", comp_name, axis_name,
units.readable_str(distance, ad.unit, sig=3))
try:
m = component.moveRel(act_mv)
try:
m.result(120)
except KeyboardInterrupt:
logging.warning("Cancelling relative move of component %s", comp_name)
m.cancel()
raise
except Exception as exc:
raise IOError("Failed to move component %s by %s: %s" %
(comp_name, act_mv, exc))
def on_paint(self, evt=None):
if not hasattr(self.Parent.canvas, 'has_data') or not self.Parent.canvas.has_data():
self.clear()
return
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
# TODO: only put label for some of the ticks
if not self.ticks:
self.calc_ticks(ctx)
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
max_width = 0
for i, (pos, val) in enumerate(self.ticks):
label = units.readable_str(val, self.unit, 3)
_, _, lbl_width, lbl_height, _, _ = ctx.text_extents(label)
if self.orientation == wx.HORIZONTAL:
lpos = pos - (lbl_width / 2)
lpos = max(min(lpos, self.ClientSize.x - lbl_width - 2), 2)
ctx.move_to(lpos, lbl_height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
else:
max_width = max(max_width, lbl_width)
lpos = pos + (lbl_height / 2)
lpos = max(min(lpos, self.ClientSize.y), 2)
ctx.move_to(self.ClientSize.x - lbl_width - 9, lpos)
ctx.show_text(label)
ctx.move_to(self.ClientSize.x - 5, pos)
ctx.line_to(self.ClientSize.x, pos)
ctx.stroke()
if self.orientation == wx.VERTICAL and max_width != self.max_tick_width:
self.max_tick_width = max_width
self.SetMinSize((self.max_tick_width + 14, -1))
self.Parent.GetSizer().Layout()
def cb_set(value, ctrl=value_ctrl, u=unit, acc=accuracy):
for i in range(ctrl.Count):
d = ctrl.GetClientData(i)
if (d == value or
(all(isinstance(v, float) for v in (value, d)) and
util.almost_equal(d, value))
):
logging.debug("Setting combobox value to %s", ctrl.Items[i])
ctrl.SetSelection(i)
break
else:
logging.debug("No existing label found for value %s in combobox ctrl %d",
value, id(ctrl))
# entering value as free text
txt = readable_str(value, u, sig=acc)
ctrl.SetValue(txt)
def _display_pretty(self):
if self._number_value is None:
str_val = u""
elif self._number_value == 0 and self.key_step and self.unit not in units.IGNORE_UNITS:
# Special case with 0: readable_str return just "0 unit", without
# prefix. This is technically correct, but quite inconvenient and
# a little strange when the typical value has a prefix (eg, nm, kV).
# => use prefix of key_step (as it's a "small value")
_, prefix = units.get_si_scale(self.key_step)
str_val = "0 %s%s" % (prefix, self.unit)
else:
str_val = units.readable_str(self._number_value, self.unit, self.accuracy)
# Get the length of the number (string length, minus the unit length)
number_length = len(str_val.rstrip(string.ascii_letters + u" µ"))
wx.TextCtrl.ChangeValue(self, str_val)
# Select the number value
wx.CallAfter(self.SetSelection, number_length, number_length)
def _display_pretty(self):
if self._number_value is None:
str_val = u""
elif self._number_value == 0 and self.key_step and self.unit not in units.IGNORE_UNITS:
# Special case with 0: readable_str return just "0 unit", without
# prefix. This is technically correct, but quite inconvenient and
# a little strange when the typical value has a prefix (eg, nm, kV).
# => use prefix of key_step (as it's a "small value")
_, prefix = units.get_si_scale(self.key_step)
str_val = "0 %s%s" % (prefix, self.unit)
else:
str_val = units.readable_str(self._number_value, self.unit,
self.accuracy)
# Get the length of the number (string length, minus the unit length)
number_length = len(str_val.rstrip(string.ascii_letters + u" µ"))
wx.TextCtrl.ChangeValue(self, str_val)
# Select the number value
wx.CallAfter(self.SetSelection, number_length, number_length)
def on_paint(self, event=None):
if not self.Parent.canvas.has_data():
self.clear()
return
if not self.ticks:
self.calc_ticks()
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx.select_font_face(
font.GetFaceName(),
cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL
)
ctx.set_font_size(font.GetPointSize())
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
for i, (pos, val) in enumerate(self.ticks):
label = units.readable_str(val, self.unit, 3)
_, _, width, height, _, _ = ctx.text_extents(label)
if self.orientation == self.HORIZONTAL:
lpos = pos - (width / 2)
lpos = max(min(lpos, self.ClientSize.x - width - 2), 2)
ctx.move_to(lpos, height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
else:
lpos = pos + (height / 2)
lpos = max(min(lpos, self.ClientSize.y - height - 2), 2)
ctx.move_to(self.ClientSize.x - width - 9, lpos)
ctx.show_text(label)
ctx.move_to(self.ClientSize.x - 5, pos)
ctx.line_to(self.ClientSize.x, pos)
ctx.stroke()
def on_paint(self, event=None):
if not self.Parent.canvas.has_data():
self.clear()
return
if not self.ticks:
self.calc_ticks()
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL,
cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
for i, (pos, val) in enumerate(self.ticks):
label = units.readable_str(val, self.unit, 3)
_, _, width, height, _, _ = ctx.text_extents(label)
if self.orientation == self.HORIZONTAL:
lpos = pos - (width / 2)
lpos = max(min(lpos, self.ClientSize.x - width - 2), 2)
ctx.move_to(lpos, height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
else:
lpos = pos + (height / 2)
lpos = max(min(lpos, self.ClientSize.y - height - 2), 2)
ctx.move_to(self.ClientSize.x - width - 9, lpos)
ctx.show_text(label)
ctx.move_to(self.ClientSize.x - 5, pos)
ctx.line_to(self.ClientSize.x, pos)
ctx.stroke()
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
try:
trans_val, cor_md = future.result()
# The magic: save the correction metadata straight into the CCD
main_data.ccd.updateMetadata(cor_md)
except CancelledError:
self._main_frame.lbl_fine_align.Label = "Cancelled"
except Exception:
logging.warning("Failed to run the fine alignment, a report "
"should be available in ~/odemis-overlay-report.")
self._main_frame.lbl_fine_align.Label = "Failed"
else:
self._main_frame.lbl_fine_align.Label = "Successful"
self._main_frame.menu_item_reset_finealign.Enable(True)
# Temporary info until the GUI can actually rotate the images
if model.MD_ROTATION_COR in cor_md:
rot = math.degrees(cor_md[model.MD_ROTATION_COR])
# the worse is the rotation, the longer it's displayed
timeout = max(2, min(abs(rot), 10))
Message.show_message(
self._main_frame,
u"Rotation applied: %s" %
(units.readable_str(rot, unit="°", sig=3)),
timeout=timeout)
logging.warning(
"Fine alignment computed rotation needed of %f°", rot)
# As the CCD image might have different pixel size, force to fit
self._main_frame.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._main_frame.btn_fine_align.Bind(wx.EVT_BUTTON,
self._on_fine_align)
self._main_frame.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._main_frame.lbl_fine_align.Show()
self._main_frame.gauge_fine_align.Hide()
self._sizer.Layout()
def move(comp_name, axis_name, str_distance):
"""
move (relatively) the axis of the given component by the specified amount of µm
"""
# for safety reason, we use µm instead of meters, as it's harder to type a
# huge distance
component = get_component(comp_name)
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" %
(comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
distance = float(str_distance) * 1e-6 # µm -> m
except ValueError:
raise ValueError("Distance '%s' cannot be converted to a number" %
str_distance)
if abs(distance) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m)" %
(abs(distance), MAX_DISTANCE))
else:
distance = convertToObject(str_distance)
try:
logging.info(u"Will move %s.%s by %s", comp_name, axis_name,
units.readable_str(distance, ad.unit, sig=3))
except Exception:
pass
try:
m = component.moveRel({axis_name: distance})
m.result()
except Exception as exc:
raise IOError("Failed to move axis %s of component %s: %s" %
(axis_name, comp_name, exc))
def move_abs(comp_name, axis_name, str_position):
"""
move (in absolute) the axis of the given component to the specified position in µm
"""
component = get_component(comp_name)
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" %
(comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
position = float(str_position)
except ValueError:
raise ValueError("Position '%s' cannot be converted to a number" %
str_position)
# compare to the current position, to see if the new position sounds reasonable
cur_pos = component.position.value[axis_name]
if abs(cur_pos - position) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m)" %
(abs(cur_pos - position), MAX_DISTANCE))
else:
position = convertToObject(str_position)
try:
logging.info(u"Will move %s.%s to %s", comp_name, axis_name,
units.readable_str(position, ad.unit, sig=3))
except Exception:
pass
try:
m = component.moveAbs({axis_name: position})
m.result()
except Exception as exc:
raise IOError("Failed to move axis %s of component %s: %s" %
(axis_name, comp_name, exc))
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
try:
trans_val, cor_md = future.result()
# The magic: save the correction metadata straight into the CCD
main_data.ccd.updateMetadata(cor_md)
except CancelledError:
self._main_frame.lbl_fine_align.Label = "Cancelled"
except Exception:
logging.warning("Failed to run the fine alignment, a report "
"should be available in ~/odemis-overlay-report.")
self._main_frame.lbl_fine_align.Label = "Failed"
else:
self._main_frame.lbl_fine_align.Label = "Successful"
self._main_frame.menu_item_reset_finealign.Enable(True)
# Temporary info until the GUI can actually rotate the images
if model.MD_ROTATION_COR in cor_md:
rot = math.degrees(cor_md[model.MD_ROTATION_COR])
# the worse is the rotation, the longer it's displayed
timeout = max(2, min(abs(rot), 10))
Message.show_message(
self._main_frame,
u"Rotation applied: %s" % (units.readable_str(rot, unit="°", sig=3)),
timeout=timeout
)
logging.warning("Fine alignment computed rotation needed of %f°",
rot)
# As the CCD image might have different pixel size, force to fit
self._main_frame.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._main_frame.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_fine_align)
self._main_frame.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._main_frame.lbl_fine_align.Show()
self._main_frame.gauge_fine_align.Hide()
self._sizer.Layout()
def move(comp_name, axis_name, str_distance):
"""
move (relatively) the axis of the given component by the specified amount of µm
"""
# for safety reason, we use µm instead of meters, as it's harder to type a
# huge distance
component = get_component(comp_name)
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
distance = float(str_distance) * 1e-6 # µm -> m
except ValueError:
raise ValueError("Distance '%s' cannot be converted to a number" %
str_distance)
if abs(distance) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m)" %
(abs(distance), MAX_DISTANCE))
else:
distance = convertToObject(str_distance)
try:
logging.info(u"Will move %s.%s by %s", comp_name, axis_name,
units.readable_str(distance, ad.unit, sig=3))
except Exception:
pass
try:
m = component.moveRel({axis_name: distance})
m.result()
except Exception as exc:
raise IOError("Failed to move axis %s of component %s: %s" %
(axis_name, comp_name, exc))
def Draw(self, dc):
# return self.DrawGC(dc)
nod = self.nod
vmiddle = self.GetClientSize()[1] // 2
background_col = self.Parent.GetBackgroundColour()
foreground_col = self.Parent.GetForegroundColour()
dc.SetBackgroundMode(wx.BRUSHSTYLE_SOLID)
dc.SetBackground(wx.Brush(background_col))
dc.Clear()
if not self.mpp: # unknown mpp => blank
return
dc.SetFont(self.GetFont())
dc.SetTextForeground(foreground_col)
dc.SetTextBackground(background_col)
length, actual = self.GetLineWidth(dc)
# Draw the text below
charSize = dc.GetTextExtent("M")
height = self.gap + charSize[1] + self.nod
main_line_y = vmiddle - (height // 2) + self.nod
dc.DrawText(units.readable_str(actual, "m", sig=2), 0,
main_line_y + self.gap)
# Draw the scale itself
pen = wx.Pen(foreground_col, self.line_width)
pen.Cap = wx.CAP_PROJECTING # how to draw the border of the lines
dc.SetPen(pen)
# main line
lines = [(0, main_line_y, length, main_line_y)]
# nods at each end
lines += [(0, main_line_y - nod, 0, main_line_y)]
lines += [(length, main_line_y - nod, length, main_line_y)]
dc.DrawLineList(lines)
def Draw(self, dc):
# return self.DrawGC(dc)
nod = self.nod
vmiddle = self.GetClientSize()[1] // 2
background_col = self.Parent.GetBackgroundColour()
foreground_col = self.Parent.GetForegroundColour()
dc.SetBackgroundMode(wx.BRUSHSTYLE_SOLID)
dc.SetBackground(wx.Brush(background_col))
dc.Clear()
if not self.mpp: # unknown mpp => blank
return
dc.SetFont(self.GetFont())
dc.SetTextForeground(foreground_col)
dc.SetTextBackground(background_col)
length, actual = self.GetLineWidth(dc)
# Draw the text below
charSize = dc.GetTextExtent("M")
height = self.gap + charSize[1] + self.nod
main_line_y = vmiddle - (height // 2) + self.nod
dc.DrawText(units.readable_str(actual, "m", sig=2),
0, main_line_y + self.gap)
# Draw the scale itself
pen = wx.Pen(foreground_col, self.line_width)
pen.Cap = wx.CAP_PROJECTING # how to draw the border of the lines
dc.SetPen(pen)
# main line
lines = [(0, main_line_y, length, main_line_y)]
# nods at each end
lines += [(0, main_line_y - nod, 0, main_line_y)]
lines += [(length, main_line_y - nod, length, main_line_y)]
dc.DrawLineList(lines)
def UpdateMagnification(self):
# TODO: shall we use the real density of the screen?
# We could use real density but how much important is it?
mppScreen = 0.00025 # 0.25 mm/px
label = u"Mag: "
# three possibilities:
# * no image => total mag (using current mpp)
# * all images have same mpp => mag instrument * mag digital
# * >1 mpp => total mag
# get all the mpps
mpps = set()
for im in self._microscope_view.stream_tree.getImages():
try:
mpps.add(im.metadata[model.MD_PIXEL_SIZE][0])
except KeyError:
pass
if len(mpps) == 1:
# two magnifications
im_mpp = mpps.pop()
magIm = mppScreen / im_mpp # as if 1 im.px == 1 sc.px
if magIm >= 1:
label += u"×" + units.readable_str(
units.round_significant(magIm, 3))
else:
label += u"÷" + units.readable_str(
units.round_significant(1.0 / magIm, 3))
magDig = im_mpp / self._microscope_view.mpp.value
if magDig >= 1:
label += u" ×" + units.readable_str(
units.round_significant(magDig, 3))
else:
label += u" ÷" + units.readable_str(
units.round_significant(1.0 / magDig, 3))
else:
# one magnification
mag = mppScreen / self._microscope_view.mpp.value
if mag >= 1:
label += u"×" + units.readable_str(
units.round_significant(mag, 3))
else:
label += u"÷" + units.readable_str(
units.round_significant(1.0 / mag, 3))
self.legend.set_mag_label(label)
def move_abs(comp_name, axis_name, str_position):
"""
move (in absolute) the axis of the given component to the specified position in µm
"""
component = get_component(comp_name)
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
if ad.unit == "m":
try:
position = float(str_position)
except ValueError:
raise ValueError("Position '%s' cannot be converted to a number" % str_position)
# compare to the current position, to see if the new position sounds reasonable
cur_pos = component.position.value[axis_name]
if abs(cur_pos - position) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m)" %
(abs(cur_pos - position), MAX_DISTANCE))
else:
position = convertToObject(str_position)
try:
logging.info(u"Will move %s.%s to %s", comp_name, axis_name,
units.readable_str(position, ad.unit, sig=3))
except Exception:
pass
try:
m = component.moveAbs({axis_name: position})
m.result()
except Exception as exc:
raise IOError("Failed to move axis %s of component %s: %s" %
(axis_name, comp_name, exc))
def test_readable_str(self):
# (input) (expected output)
values = [
((1.0, None), "1"),
((1, None), "1"),
((-1.234, "m"), "-1.234 m"),
((-1234, "g"), "-1.234 kg"),
((160000, None), "160000"),
((-1600, "N"), "-1.6 kN"),
((-1601, "N", 3), "-1.6 kN"), # sig=3
((0.0001236, None), "0.0001236"),
((0.0012, "V"), "1.2 mV"),
((200e-6, "m"), u"200 µm"),
((0.0, "m"), "0 m"),
(([1500, 1200, 150], None), "1500 x 1200 x 150"),
(([0.0001236, 0.00014], "m"), u"123.6 x 140 µm"),
(([0.0001236, 12.0], "m"), "0.0001236 x 12 m"),
(([1200,
1000], "px"), "1200 x 1000 px"), # special non-prefix unit
]
for (i, eo) in values:
o = units.readable_str(*i)
self.assertEquals(o, eo,
u"%s is '%s' while expected '%s'" % (i, o, eo))
def UpdateMagnification(self):
# TODO: shall we use the real density of the screen?
# We could use real density but how much important is it?
mppScreen = 0.00025 # 0.25 mm/px
label = u"Mag: "
# three possibilities:
# * no image => total mag (using current mpp)
# * all images have same mpp => mag instrument * mag digital
# * >1 mpp => total mag
# get all the mpps
mpps = set()
for im in self._microscope_view.stream_tree.getImages():
try:
mpps.add(im.metadata[model.MD_PIXEL_SIZE][0])
except KeyError:
pass
if len(mpps) == 1:
# two magnifications
im_mpp = mpps.pop()
magIm = mppScreen / im_mpp # as if 1 im.px == 1 sc.px
if magIm >= 1:
label += u"×" + units.readable_str(units.round_significant(magIm, 3))
else:
label += u"÷" + units.readable_str(units.round_significant(1.0 / magIm, 3))
magDig = im_mpp / self._microscope_view.mpp.value
if magDig >= 1:
label += u" ×" + units.readable_str(units.round_significant(magDig, 3))
else:
label += u" ÷" + units.readable_str(units.round_significant(1.0 / magDig, 3))
else:
# one magnification
mag = mppScreen / self._microscope_view.mpp.value
if mag >= 1:
label += u"×" + units.readable_str(units.round_significant(mag, 3))
else:
label += u"÷" + units.readable_str(units.round_significant(1.0 / mag, 3))
self.legend.set_mag_label(label)
def _runAcquisition(self, future):
self._data = []
self._md = {}
wls = self.startWavelength.value
wle = self.endWavelength.value
res = self.numberOfPixels.value
dt = self.dwellTime.value
trig = self._detector.softwareTrigger
df = self._detector.data
# Prepare the hardware
self._emitter.resolution.value = (1, 1) # Force one pixel only
self._emitter.translation.value = self.emtTranslation.value
self._emitter.dwellTime.value = dt
df.synchronizedOn(trig)
df.subscribe(self._on_mchr_data)
wllist = []
if wle == wls:
res = 1
if res <= 1:
res = 1
wli = 0
else:
wli = (wle - wls) / (res - 1)
try:
for i in range(res):
left = (res - i) * (dt + 0.05)
future.set_progress(end=time.time() + left)
cwl = wls + i * wli # requested value
self._sgr.moveAbs({"wavelength": cwl}).result()
if future._acq_state == CANCELLED:
raise CancelledError()
cwl = self._sgr.position.value["wavelength"] # actual value
logging.info("Acquiring point %d/%d @ %s", i + 1, res,
units.readable_str(cwl, unit="m", sig=3))
self._pt_acq.clear()
trig.notify()
if not self._pt_acq.wait(dt * 5 + 1):
raise IOError("Timeout waiting for the data")
if future._acq_state == CANCELLED:
raise CancelledError()
wllist.append(cwl)
# Done
df.unsubscribe(self._on_mchr_data)
df.synchronizedOn(None)
# Convert the sequence of data into one spectrum in a DataArray
if wls > wle: # went backward? => sort back the spectrum
logging.debug("Inversing spectrum as acquisition went from %g to %g m", wls, wls)
self._data.reverse()
wllist.reverse()
na = numpy.array(self._data) # keeps the dtype
na.shape += (1, 1, 1, 1) # make it 5th dim to indicate a channel
md = self._md
md[model.MD_WL_LIST] = wllist
if model.MD_OUT_WL in md:
# The MD_OUT_WL on the monochromator contains the current cw, which we don't want
del md[model.MD_OUT_WL]
# MD_POS should already be at the correct position (from the e-beam metadata)
# MD_PIXEL_SIZE is not meaningful but handy for the display in Odemis
# (it's the size of the square on top of the SEM survey => BIG!)
sempxs = self._emitter.pixelSize.value
md[model.MD_PIXEL_SIZE] = (sempxs[0] * 50, sempxs[1] * 50)
spec = model.DataArray(na, md)
with future._acq_lock:
if future._acq_state == CANCELLED:
raise CancelledError()
future._acq_state = FINISHED
return [spec]
except CancelledError:
raise # Just don't log the exception
except Exception:
logging.exception("Failure during monochromator scan")
finally:
# In case it was stopped before the end
df.unsubscribe(self._on_mchr_data)
df.synchronizedOn(None)
future._acq_done.set()
def on_paint(self, _):
if self._value_range is None:
return
# shared function with the export method
self._tick_list, self._vtp_ratio = calculate_ticks(self._value_range, self.ClientSize, self._orientation, self._tick_spacing)
csize = self.ClientSize
if self.lock_va is not None and self.lock_va.value == False:
if self._orientation == wx.HORIZONTAL:
csize.x -= 24
# If min and max are very close, we need more significant numbers to
# ensure the values displayed are different (ex 17999 -> 18003)
rng = self._value_range
if rng[0] == rng[1]:
sig = None
else:
ratio_rng = max(abs(v) for v in rng) / (max(rng) - min(rng))
sig = max(3, 1 + math.ceil(math.log10(ratio_rng * len(self._tick_list))))
# Set Font
font = wx.SystemSettings.GetFont(wx.SYS_DEFAULT_GUI_FONT)
ctx = wx.lib.wxcairo.ContextFromDC(wx.PaintDC(self))
ctx.select_font_face(font.GetFaceName(), cairo.FONT_SLANT_NORMAL, cairo.FONT_WEIGHT_NORMAL)
ctx.set_font_size(font.GetPointSize())
ctx.set_source_rgb(*self.tick_colour)
ctx.set_line_width(2)
ctx.set_line_join(cairo.LINE_JOIN_MITER)
max_width = 0
prev_lpos = 0 if self._orientation == wx.HORIZONTAL else csize.y
for i, (pos, val) in enumerate(self._tick_list):
label = units.readable_str(val, self.unit, sig)
if i == 0 and self._lo_ellipsis:
label = u"…" + label
if i == len(self._tick_list) - 1 and self._hi_ellipsis:
label = label + u"…"
_, _, lbl_width, lbl_height, _, _ = ctx.text_extents(label)
if self._orientation == wx.HORIZONTAL:
lpos = pos - (lbl_width // 2)
lpos = max(min(lpos, csize.x - lbl_width - 2), 2)
# print (i, prev_right, lpos)
if prev_lpos < lpos:
ctx.move_to(lpos, lbl_height + 8)
ctx.show_text(label)
ctx.move_to(pos, 5)
ctx.line_to(pos, 0)
prev_lpos = lpos + lbl_width
else:
max_width = max(max_width, lbl_width)
lpos = pos + (lbl_height // 2)
lpos = max(min(lpos, csize.y), 2)
if prev_lpos >= lpos + 20 or i == 0:
ctx.move_to(csize.x - lbl_width - 9, lpos)
ctx.show_text(label)
ctx.move_to(csize.x - 5, pos)
ctx.line_to(csize.x, pos)
prev_lpos = lpos + lbl_height
ctx.stroke()
if self._orientation == wx.VERTICAL and max_width != self._max_tick_width:
self._max_tick_width = max_width
self.SetMinSize((self._max_tick_width + 14, -1))
self.Parent.GetSizer().Layout()
def _runAcquisition(self, future):
self._data = []
self._md = {}
wls = self.startWavelength.value
wle = self.endWavelength.value
res = self.numberOfPixels.value
dt = self.dwellTime.value
trig = self._detector.softwareTrigger
df = self._detector.data
# Prepare the hardware
self._emitter.resolution.value = (1, 1) # Force one pixel only
self._emitter.translation.value = self.emtTranslation.value
self._emitter.dwellTime.value = dt
df.synchronizedOn(trig)
df.subscribe(self._on_mchr_data)
wllist = []
if wle == wls:
res = 1
if res <= 1:
res = 1
wli = 0
else:
wli = (wle - wls) / (res - 1)
try:
for i in range(res):
left = (res - i) * (dt + 0.05)
future.set_progress(end=time.time() + left)
cwl = wls + i * wli # requested value
self._sgr.moveAbs({"wavelength": cwl}).result()
if future._acq_state == CANCELLED:
raise CancelledError()
cwl = self._sgr.position.value["wavelength"] # actual value
logging.info("Acquiring point %d/%d @ %s", i + 1, res,
units.readable_str(cwl, unit="m", sig=3))
self._pt_acq.clear()
trig.notify()
if not self._pt_acq.wait(dt * 5 + 1):
raise IOError("Timeout waiting for the data")
if future._acq_state == CANCELLED:
raise CancelledError()
wllist.append(cwl)
# Done
df.unsubscribe(self._on_mchr_data)
df.synchronizedOn(None)
# Convert the sequence of data into one spectrum in a DataArray
if wls > wle: # went backward? => sort back the spectrum
logging.debug(
"Inverting spectrum as acquisition went from %g to %g m",
wls, wls)
self._data.reverse()
wllist.reverse()
na = numpy.array(self._data) # keeps the dtype
na.shape += (1, 1, 1, 1) # make it 5th dim to indicate a channel
md = self._md
md[model.MD_WL_LIST] = wllist
if model.MD_OUT_WL in md:
# The MD_OUT_WL on the monochromator contains the current cw, which we don't want
del md[model.MD_OUT_WL]
# MD_POS should already be at the correct position (from the e-beam metadata)
# MD_PIXEL_SIZE is not meaningful but handy for the display in Odemis
# (it's the size of the square on top of the SEM survey => BIG!)
sempxs = self._emitter.pixelSize.value
md[model.MD_PIXEL_SIZE] = (sempxs[0] * 50, sempxs[1] * 50)
spec = model.DataArray(na, md)
with future._acq_lock:
if future._acq_state == CANCELLED:
raise CancelledError()
future._acq_state = FINISHED
return [spec]
except CancelledError:
raise # Just don't log the exception
except Exception:
logging.exception("Failure during monochromator scan")
finally:
# In case it was stopped before the end
df.unsubscribe(self._on_mchr_data)
df.synchronizedOn(None)
future._acq_done.set()
def value_formatter(value, unit=val_unit):
value_ctrl.SetValue(readable_str(value, unit, sig=sig))
def move_abs(comp_name, moves, check_distance=True):
"""
move (in absolute) the axis of the given component to the specified position
comp_name (str): name of the component
check_distance (bool): if the axis is in meters, check that the move is not
too big.
moves (dict str -> str): axis -> position (as text)
"""
component = get_component(comp_name)
act_mv = {} # axis -> value
for axis_name, str_position in moves.items():
try:
if axis_name not in component.axes:
raise ValueError("Actuator %s has no axis '%s'" % (comp_name, axis_name))
ad = component.axes[axis_name]
except (TypeError, AttributeError):
raise ValueError("Component %s is not an actuator" % comp_name)
# Allow the user to indicate the position via the user-friendly choice entry
position = None
if (hasattr(ad, "choices") and isinstance(ad.choices, dict)):
for key, value in ad.choices.items():
if value == str_position:
logging.info("Converting '%s' into %s", str_position, key)
position = key
# Even if it's a big distance, we don't complain as it's likely
# that all choices are safe
break
if position is None:
if ad.unit == "m":
try:
position = float(str_position)
except ValueError:
raise ValueError("Position '%s' cannot be converted to a number" % str_position)
# compare to the current position, to see if the new position sounds reasonable
cur_pos = component.position.value[axis_name]
if check_distance and abs(cur_pos - position) > MAX_DISTANCE:
raise IOError("Distance of %f m is too big (> %f m), use '--big-distance' to allow the move." %
(abs(cur_pos - position), MAX_DISTANCE))
else:
position = convert_to_object(str_position)
# If only a couple of positions are possible, and asking for a float,
# avoid the rounding error by looking for the closest possible
if (isinstance(position, numbers.Real) and
hasattr(ad, "choices") and
isinstance(ad.choices, collections.Iterable) and
position not in ad.choices):
closest = util.find_closest(position, ad.choices)
if util.almost_equal(closest, position, rtol=1e-3):
logging.debug("Adjusting value %.15g to %.15g", position, closest)
position = closest
act_mv[axis_name] = position
logging.info(u"Will move %s.%s to %s", comp_name, axis_name,
units.readable_str(position, ad.unit, sig=3))
try:
m = component.moveAbs(act_mv)
try:
m.result(120)
except KeyboardInterrupt:
logging.warning("Cancelling absolute move of component %s", comp_name)
m.cancel()
raise
except Exception as exc:
raise IOError("Failed to move component %s to %s: %s" %
(comp_name, act_mv, exc))
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
self._acq_future = None # To avoid holding the ref in memory
self._faf_connector = None
try:
# DEBUG
try:
trans_val, cor_md = future.result()
except Exception:
cor_md = {}, {}
opt_md, sem_md = cor_md
# Save the optical correction metadata straight into the CCD
main_data.ccd.updateMetadata(opt_md)
# The SEM correction metadata goes to the ebeam
main_data.ebeam.updateMetadata(sem_md)
except CancelledError:
self._tab_panel.lbl_fine_align.Label = "Cancelled"
except Exception as ex:
logging.warning("Failure during overlay: %s", ex)
self._tab_panel.lbl_fine_align.Label = "Failed"
else:
self._main_frame.menu_item_reset_finealign.Enable(True)
# Check whether the values make sense. If not, we still accept them,
# but hopefully make it clear enough to the user that the calibration
# should not be trusted.
rot = opt_md.get(model.MD_ROTATION_COR, 0)
rot0 = (rot + math.pi) % (2 *
math.pi) - math.pi # between -pi and pi
rot_deg = math.degrees(rot0)
opt_scale = opt_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))[0]
shear = sem_md.get(model.MD_SHEAR_COR, 0)
scaling_xy = sem_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))
if (not abs(rot_deg) < 10 or # Rotation < 10°
not 0.9 < opt_scale < 1.1 or # Optical mag < 10%
not abs(shear) < 0.3 or # Shear < 30%
any(not 0.9 < v < 1.1
for v in scaling_xy) # SEM ratio diff < 10%
):
# Special warning in case of wrong magnification
if not 0.9 < opt_scale < 1.1 and model.hasVA(
main_data.lens, "magnification"):
lens_mag = main_data.lens.magnification.value
measured_mag = lens_mag / opt_scale
logging.warning(
"The measured optical magnification is %fx, instead of expected %fx. "
"Check that the lens magnification and the SEM magnification are correctly set.",
measured_mag, lens_mag)
else: # Generic warning
logging.warning(
u"The fine alignment values are very large, try on a different place on the sample. "
u"mag correction: %f, rotation: %f°, shear: %f, X/Y scale: %f",
opt_scale, rot_deg, shear, scaling_xy)
self._tab_panel.lbl_fine_align.Label = "Probably incorrect"
else:
self._tab_panel.lbl_fine_align.Label = "Successful"
# Rotation is compensated in software on the FM image, but the user
# can also change the SEM scan rotation, and re-run the alignment,
# so show it clearly, for the user to take action.
# The worse the rotation, the longer it's displayed.
timeout = max(2, min(abs(rot_deg), 10))
popup.show_message(
self._tab_panel,
u"Rotation applied: %s\nShear applied: %s\nX/Y Scaling applied: %s"
% (units.readable_str(
rot_deg, unit=u"°", sig=3), units.readable_str(
shear, sig=3), units.readable_str(scaling_xy, sig=3)),
timeout=timeout)
logging.info(
u"Fine alignment computed mag correction of %f, rotation of %f°, "
u"shear needed of %s, and X/Y scaling needed of %s.",
opt_scale, rot, shear, scaling_xy)
# As the CCD image might have different pixel size, force to fit
self._tab_panel.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._tab_panel.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_fine_align)
self._tab_panel.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._tab_panel.lbl_fine_align.Show()
self._tab_panel.gauge_fine_align.Hide()
self._sizer.Layout()
def _on_fa_done(self, future):
logging.debug("End of overlay procedure")
main_data = self._main_data_model
self._acq_future = None # To avoid holding the ref in memory
self._faf_connector = None
try:
# DEBUG
try:
trans_val, cor_md = future.result()
except Exception:
cor_md = {}, {}
opt_md, sem_md = cor_md
# Save the optical correction metadata straight into the CCD
main_data.ccd.updateMetadata(opt_md)
# The SEM correction metadata goes to the ebeam
main_data.ebeam.updateMetadata(sem_md)
except CancelledError:
self._tab_panel.lbl_fine_align.Label = "Cancelled"
except Exception as ex:
logging.warning("Failure during overlay: %s", ex)
self._tab_panel.lbl_fine_align.Label = "Failed"
else:
self._main_frame.menu_item_reset_finealign.Enable(True)
# Check whether the values make sense. If not, we still accept them,
# but hopefully make it clear enough to the user that the calibration
# should not be trusted.
rot = opt_md.get(model.MD_ROTATION_COR, 0)
rot0 = (rot + math.pi) % (2 * math.pi) - math.pi # between -pi and pi
rot_deg = math.degrees(rot0)
opt_scale = opt_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))[0]
shear = sem_md.get(model.MD_SHEAR_COR, 0)
scaling_xy = sem_md.get(model.MD_PIXEL_SIZE_COR, (1, 1))
if (not abs(rot_deg) < 10 or # Rotation < 10°
not 0.9 < opt_scale < 1.1 or # Optical mag < 10%
not abs(shear) < 0.3 or # Shear < 30%
any(not 0.9 < v < 1.1 for v in scaling_xy) # SEM ratio diff < 10%
):
# Special warning in case of wrong magnification
if not 0.9 < opt_scale < 1.1 and model.hasVA(main_data.lens, "magnification"):
lens_mag = main_data.lens.magnification.value
measured_mag = lens_mag / opt_scale
logging.warning("The measured optical magnification is %fx, instead of expected %fx. "
"Check that the lens magnification and the SEM magnification are correctly set.",
measured_mag, lens_mag)
else: # Generic warning
logging.warning(u"The fine alignment values are very large, try on a different place on the sample. "
u"mag correction: %f, rotation: %f°, shear: %f, X/Y scale: %f",
opt_scale, rot_deg, shear, scaling_xy)
self._tab_panel.lbl_fine_align.Label = "Probably incorrect"
else:
self._tab_panel.lbl_fine_align.Label = "Successful"
# Rotation is compensated in software on the FM image, but the user
# can also change the SEM scan rotation, and re-run the alignment,
# so show it clearly, for the user to take action.
# The worse the rotation, the longer it's displayed.
timeout = max(2, min(abs(rot_deg), 10))
popup.show_message(
self._tab_panel,
u"Rotation applied: %s\nShear applied: %s\nX/Y Scaling applied: %s"
% (units.readable_str(rot_deg, unit=u"°", sig=3),
units.readable_str(shear, sig=3),
units.readable_str(scaling_xy, sig=3)),
timeout=timeout
)
logging.info(u"Fine alignment computed mag correction of %f, rotation of %f°, "
u"shear needed of %s, and X/Y scaling needed of %s.",
opt_scale, rot, shear, scaling_xy)
# As the CCD image might have different pixel size, force to fit
self._tab_panel.vp_align_ccd.canvas.fit_view_to_next_image = True
main_data.is_acquiring.value = False
self._tab_panel.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_fine_align)
self._tab_panel.btn_fine_align.Label = self._fa_btn_label
self._resume()
self._tab_panel.lbl_fine_align.Show()
self._tab_panel.gauge_fine_align.Hide()
self._sizer.Layout()
def _display_pretty(self):
if self._number_value is None:
str_val = u""
else:
str_val = units.readable_str(self._number_value, sig=self.accuracy)
wx.TextCtrl.ChangeValue(self, str_val)
def _display_pretty(self):
if self._number_value is None:
str_val = u""
else:
str_val = units.readable_str(self._number_value, sig=self.accuracy)
wx.TextCtrl.ChangeValue(self, str_val)
