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m to pixels
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@K4rishma
K4rishma committed Jan 27, 2025
1 parent 6f46212 commit afd8efa
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Showing 3 changed files with 72 additions and 91 deletions.
111 changes: 35 additions & 76 deletions src/odemis/gui/comp/overlay/cryo_feature.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
from odemis.gui.comp.overlay.base import DragMixin, WorldOverlay
from odemis.gui.comp.overlay.stage_point_select import StagePointSelectOverlay
from odemis.gui.model import TOOL_FEATURE, TOOL_NONE, TOOL_FIDUCIAL, TOOL_REGION_OF_INTEREST
from odemis.gui.util.conversion import pixel_pos_to_canvas_pos, canvas_pos_to_pixel_pos

MODE_EDIT_FEATURES = 1
MODE_SHOW_FEATURES = 2
Expand Down Expand Up @@ -425,10 +426,9 @@ def _update_selected_target_position(self, v_pos):
Update the selected target with the newly moved position
:param v_pos: (int, int) the coordinates in the view
"""
p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
# todo
self._selected_target.coordinates.value = tuple((p_pos[0], p_pos[1], 0)) #Todo
# Reset the selected tool to signal end of target moving operation
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size()), 1e-07)
self._selected_feature.pos.value = [p_pos[0], p_pos[1], self._selected_feature.pos.value[2]]
# Reset the selected tool to signal end of feature moving operation
# self._selected_tool_va.value = TOOL_NONE
self.cnvs.update_drawing()

Expand All @@ -439,62 +439,13 @@ def _detect_point_inside_target(self, v_pos):
:return: (CryoFeature or None) Found target, None if not found
"""

def in_radius(c_x, c_y, r, x, y):
return math.hypot(c_x - x, c_y - y) <= r

offset = self.cnvs.get_half_buffer_size() # to convert physical target positions to pixels
for target in self.tab_data.main.targets.value:
coordinates = target.coordinates.value
fvsp = self.cnvs.phys_to_view(coordinates, offset)
if in_radius(fvsp[0], fvsp[1], FEATURE_DIAMETER, v_pos[0], v_pos[1]):
return target
pass

def draw(self, ctx, shift=(0, 0), scale=1.0):
"""
Draw all the targets, on their location, indicating their status and whether it's selected or hovered on.
"""
return
if not self.show:
return


# Check if the current view is "FLM Overview"
# if hasattr(self.tab_data, "focussedView"):
# current_view = self.tab_data.focussedView.value.name.value
# if current_view != "SEM Overview":
# return

# Show each target icon and label if applicable
for target in self.tab_data.main.targets.value:
coordinates = target.coordinates.value
half_size_offset = self.cnvs.get_half_buffer_size()

# convert physical position to buffer 'world' coordinates
bpos = self.cnvs.phys_to_buffer_pos((coordinates[0], coordinates[1]), self.cnvs.p_buffer_center, self.cnvs.scale,
offset=half_size_offset)

def set_icon(feature_icon):
ctx.set_source_surface(feature_icon, bpos[0] - FEATURE_ICON_CENTER, bpos[1] - FEATURE_ICON_CENTER)

# Show proper feature icon based on selected target + status
try:
if target is self.tab_data.main.currentTarget.value:
set_icon(self._feature_icons_selected[target.type.value])
# set_icon(self._feature_icons_selected[target.status.value])
else:
set_icon(self._feature_icons[target.type.value])
# set_icon(self._feature_icons[target.status.value])
except KeyError:
raise
# logging.error("Feature status for feature {} is not one of the predefined statuses.".format(feature.name.value))

if target is self._hover_target:
# show target name on hover
self._label.text = target.name.value # str(target.index.value)
self._label.pos = (bpos[0], bpos[1])
self._label.draw(ctx)

ctx.paint()
pass

class CryoCorrelationFmPointsOverlay(CryoCorrelationPointsOverlay):

Expand All @@ -511,7 +462,7 @@ def in_radius(c_x, c_y, r, x, y):
offset = self.cnvs.get_half_buffer_size() # to convert physical target positions to pixels
for target in self.tab_data.main.targets.value:
if "FM" in target.name.value or "POI" in target.name.value:
coordinates = target.coordinates.value
coordinates = pixel_pos_to_canvas_pos(target.coordinates.value, scale = 1e-07)
fvsp = self.cnvs.phys_to_view(coordinates, offset)
if in_radius(fvsp[0], fvsp[1], FEATURE_DIAMETER, v_pos[0], v_pos[1]):
return target
Expand All @@ -533,11 +484,13 @@ def on_left_down(self, evt):
self.cnvs.set_dynamic_cursor(gui.DRAG_CURSOR)
else:
# create new target based on the physical position then disable the target tool
p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size()),
1e-07)
# p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
# if self.tab_data.main.selected_target_type is None:
# self.tab_data.main.selected_target_type.value = "Fiducial"
self.tab_data.add_new_target(p_pos[0], p_pos[1],
type=self.tab_data.main.selected_target_type.value) # TODO
type=self.tab_data.main.selected_target_type.value)
# self._selected_tool_va.value = TOOL_NONE

else:
Expand Down Expand Up @@ -582,10 +535,10 @@ def on_motion(self, evt):
if self.left_dragging:
self.cnvs.set_dynamic_cursor(gui.DRAG_CURSOR)
DragMixin._on_motion(self, evt)
p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size()), 1e-07)
# p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
# self._selected_target = self.tab_data.main.currentTarget.value
self._selected_target.coordinates.value = tuple(
(p_pos[0], p_pos[1], 0)) # TODO self._selected_target.coordinates.value[2]))
self._selected_target.coordinates.value = [p_pos[0], p_pos[1], self._selected_target.coordinates.value[2]]
self.cnvs.update_drawing()
return
target = self._detect_point_inside_target(v_pos)
Expand Down Expand Up @@ -619,7 +572,8 @@ def draw(self, ctx, shift=(0, 0), scale=1.0):
# Show each target icon and label if applicable
for target in self.tab_data.main.targets.value:
if "FM" in target.name.value or "POI" in target.name.value:
coordinates = target.coordinates.value
coordinates = pixel_pos_to_canvas_pos(target.coordinates.value, scale=1e-07)
# coordinates = target.coordinates.value
half_size_offset = self.cnvs.get_half_buffer_size()

# convert physical position to buffer 'world' coordinates
Expand Down Expand Up @@ -668,7 +622,8 @@ def in_radius(c_x, c_y, r, x, y):
offset = self.cnvs.get_half_buffer_size() # to convert physical target positions to pixels
for target in self.tab_data.main.targets.value:
if "FIB" in target.name.value:
coordinates = target.coordinates.value
coordinates = pixel_pos_to_canvas_pos(target.coordinates.value, scale=1e-07)
# coordinates = target.coordinates.value
fvsp = self.cnvs.phys_to_view(coordinates, offset)
if in_radius(fvsp[0], fvsp[1], FEATURE_DIAMETER, v_pos[0], v_pos[1]):
return target
Expand All @@ -680,13 +635,13 @@ def on_motion(self, evt):
if self.left_dragging:
self.cnvs.set_dynamic_cursor(gui.DRAG_CURSOR)
DragMixin._on_motion(self, evt)
p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size()), 1e-07)
# p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
if self._mode == MODE_EDIT_REFRACTIVE_INDEX:
self.tab_data.fib_surface_point.value.coordinates.value = tuple(
(p_pos[0], p_pos[1], 0))
self.tab_data.fib_surface_point.value.coordinates.value = [p_pos[0], p_pos[1], int(0)]
# self._selected_target = self.tab_data.main.currentTarget.value
else:
self._selected_target.coordinates.value = tuple((p_pos[0], p_pos[1], 0)) # TODO self._selected_target.coordinates.value[2]))
self._selected_target.coordinates.value = [p_pos[0], p_pos[1], self._selected_target.coordinates.value[2]]
self.cnvs.update_drawing()
return
target = self._detect_point_inside_target(v_pos)
Expand All @@ -711,13 +666,13 @@ def on_left_down(self, evt):
if self.active.value:
v_pos = evt.Position
target = self._detect_point_inside_target(v_pos)
p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size()), 1e-07)
# p_pos = self.cnvs.view_to_phys(v_pos, self.cnvs.get_half_buffer_size())
if self._mode == MODE_EDIT_REFRACTIVE_INDEX:
# Todo what does mode do
if self.tab_data.fib_surface_point.value:
# add/modify fib_surface_fiducial
self.tab_data.fib_surface_point.value.coordinates.value = tuple(
(p_pos[0], p_pos[1], 0)) # TODO self._selected_target.coordinates.value[2]))
self.tab_data.fib_surface_point.value.coordinates.value = [p_pos[0], p_pos[1], int(0)]
self.cnvs.set_dynamic_cursor(gui.DRAG_CURSOR)
else:
self.tab_data.add_new_target(p_pos[0], p_pos[1], type=self.tab_data.main.selected_target_type.value)
Expand Down Expand Up @@ -761,9 +716,10 @@ def on_left_up(self, evt):
if self.left_dragging:
#TODO separate concerns if and else are not looking for same conditiond
if self._mode == MODE_EDIT_REFRACTIVE_INDEX:
p_pos = self.cnvs.view_to_phys(evt.Position, self.cnvs.get_half_buffer_size())
self.tab_data.fib_surface_point.value.coordinates.value = tuple(
(p_pos[0], p_pos[1], 0)) # TODO self._selected_target.coordinates.value[2]))
p_pos = canvas_pos_to_pixel_pos(self.cnvs.view_to_phys(evt.Position, self.cnvs.get_half_buffer_size()),
1e-07)
# p_pos = self.cnvs.view_to_phys(evt.Position, self.cnvs.get_half_buffer_size())
self.tab_data.fib_surface_point.value.coordinates.value = [p_pos[0], p_pos[1], int(0)]
self.cnvs.update_drawing()
else:
if self._selected_target:
Expand Down Expand Up @@ -791,7 +747,8 @@ def draw(self, ctx, shift=(0, 0), scale=1.0):
# Show each target icon and label if applicable
for target in self.tab_data.main.targets.value:
if "FIB" in target.name.value:# or "Projected" in target.name.value:
coordinates = target.coordinates.value
coordinates = pixel_pos_to_canvas_pos(target.coordinates.value, scale=1e-07)
# coordinates = target.coordinates.value
half_size_offset = self.cnvs.get_half_buffer_size()

# convert physical position to buffer 'world' coordinates
Expand Down Expand Up @@ -826,7 +783,8 @@ def set_icon(feature_icon):
ctx.paint()

if self.tab_data.fib_surface_point.value:
coordinates = self.tab_data.fib_surface_point.value.coordinates.value
coordinates = pixel_pos_to_canvas_pos(self.tab_data.fib_surface_point.value.coordinates.value, scale=1e-07)
# coordinates = self.tab_data.fib_surface_point.value.coordinates.value
half_size_offset = self.cnvs.get_half_buffer_size()
bpos = self.cnvs.phys_to_buffer_pos((coordinates[0], coordinates[1]), self.cnvs.p_buffer_center,
self.cnvs.scale,
Expand All @@ -839,7 +797,8 @@ def set_icon(feature_icon):
ctx.paint()

for target in self.tab_data.projected_points:
coordinates = target.coordinates.value
coordinates = pixel_pos_to_canvas_pos(target.coordinates.value, scale=1e-07)
# coordinates = target.coordinates.value
half_size_offset = self.cnvs.get_half_buffer_size()

# convert physical position to buffer 'world' coordinates
Expand Down
32 changes: 17 additions & 15 deletions src/odemis/gui/cont/correlation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -487,7 +487,10 @@ class GridColumns(Enum):

DEBUG = False
class CorrelationPointsController(object):

# TODO reset output
# save and show output
# POI > 1
# xyz changes
def __init__(self, tab_data, panel, tab, viewports):
"""
:param tab_data: (MicroscopyGUIData) the representation of the microscope GUI
Expand Down Expand Up @@ -546,9 +549,9 @@ def __init__(self, tab_data, panel, tab, viewports):
# Set column labels for correlation points
# Set the data type and if the column can be edited
self.grid.SetColLabelValue(GridColumns.Type.value, GridColumns.Type.name)
attr = wx.grid.GridCellAttr()
attr.SetReadOnly(True)
self.grid.SetColAttr(0, attr)
# attr = wx.grid.GridCellAttr()
# attr.SetReadOnly(True)
# self.grid.SetColAttr(0, attr)
# self.grid.SetColLabelValue(1, "X")
# self.grid.SetColLabelValue(2, "Y")
# self.grid.SetColLabelValue(3, "Z")
Expand Down Expand Up @@ -934,11 +937,12 @@ def on_cell_changing(self, event):
vp.canvas.update_drawing()
# Todo KEEP 1 POI IN CRYO_FEATURE
# \TODO pos load error
# pencin in fib view
except ValueError:
wx.MessageBox("Index must be a int!", "Invalid Input", wx.OK | wx.ICON_ERROR)
event.Veto() # Prevent the change
return
elif col_name in [GridColumns.X.name, GridColumns.Y.name, GridColumns.Z.name]:
elif col_name in [GridColumns.X.name, GridColumns.Y.name]: #, GridColumns.Z.name]:
try:
p = float(new_value)
# if Z and FIB target, do not allow the change, before calling this function TODO
Expand Down Expand Up @@ -1015,7 +1019,7 @@ def _on_current_coordinates_changes(self, coordinates):
# self.grid.SelectRow(row)
self.grid.SetCellValue(row, GridColumns.X.value, str(target.coordinates.value[0]))
self.grid.SetCellValue(row, GridColumns.Y.value, str(target.coordinates.value[1]))
if target.coordinates.value[2]:
if "FIB" not in target.name.value:
self.grid.SetCellValue(row, GridColumns.Z.value, str(target.coordinates.value[2]))

self.update_feature_correlation_target()
Expand Down Expand Up @@ -1075,16 +1079,14 @@ def _on_target_changes(self, targets):
self.grid.SetCellValue(current_row_count, GridColumns.X.value, str(target.coordinates.value[0]))
self.grid.SetCellValue(current_row_count, GridColumns.Y.value, str(target.coordinates.value[1]))
self.grid.SetCellValue(current_row_count, GridColumns.Index.value, str(target.index.value))
self.grid.SetCellValue(current_row_count, GridColumns.Type.value, target.name.value)


if "FIB" in target.name.value:
self.grid.SetCellValue(current_row_count, GridColumns.Z.value, "")
else:
self.grid.SetCellValue(current_row_count, GridColumns.Z.value, str(target.coordinates.value[2]))

if target.type.value == "Fiducial":
if target.coordinates.value[2]:
self.grid.SetCellValue(current_row_count, GridColumns.Type.value, target.name.value)
self.grid.SetCellValue(current_row_count, GridColumns.Z.value, str(target.coordinates.value[2]))
else:
self.grid.SetCellValue(current_row_count, GridColumns.Type.value, target.name.value)
self.grid.SetCellValue(current_row_count, GridColumns.Z.value, "")
elif target.type.value == "RegionOfInterest":
self.grid.SetCellValue(current_row_count, GridColumns.Type.value, target.name.value)

# self.grid.Layout()
self.reorder_table()
Expand Down
20 changes: 20 additions & 0 deletions src/odemis/gui/util/conversion.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,26 @@
from odemis.util.conversion import (frgb_to_rgb, hex_to_frgb, hex_to_rgb,
rgb_to_frgb)

def canvas_pos_to_pixel_pos(canvas_pos, scale, offset=(0, 0)):
""" Convert canvas position to pixel position
:param canvas_pos: (float, float)
:param scale: float
:param offset: (float, float)
:return: (float, float)
"""
return ((canvas_pos[0] - offset[0]) / scale,
(canvas_pos[1] - offset[1]) / scale)

def pixel_pos_to_canvas_pos(pixel_pos, scale, offset = (0,0)):
""" Convert pixel position to canvas position
:param pixel_pos: (float, float)
:param scale: float
:param offset: (float, float)
:return: (float, float)
"""
return (pixel_pos[0] * scale + offset[0],
pixel_pos[1] * scale + offset[1])


def wxcol_to_rgb(wxcol):
""" Convert a wx.Colour to an RGB int tuple
Expand Down

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