Selection Module
flyqma.selection
provides a matplotlib-based GUI for defining a region of interest within each image.
User Interface
Tools for constructing a layer and stack selection GUI.
-
class
flyqma.selection.interface.
LayerInterface
(layer, axes)[source]
Event handler for an individual layer.
Attributes:
include (bool) - flag for layer inclusion
active_polyhon (bool) - if True, polygon is currently active
pts (list) - selection boundary points
traceback (list) - exception traceback
Inherited attributes:
path (str) - layer path
layer (flyqma.Layer) - layer instance
axes (array like) - axes for blue/red/green color channels
-
add_point
(pt)[source]
Add point to layer selection bounds.
-
clear
()[source]
Clear all points from layer selection bounds.
-
load
()[source]
Load layer selection.
-
remove_point
()[source]
Remove last point added to layer selection bounds.
-
save
()[source]
Save selected points and selection metadata to file.
-
undo
()[source]
Remove last point added and update polygon.
-
update_polygon
()[source]
Update polygon for each image.
-
class
flyqma.selection.interface.
LayerVisualization
(layer, axes)[source]
Object for visualizing a single layer.
Attributes:
path (str) - layer path
layer (flyqma.Layer) - layer instance
axes (array like) - axes for blue/red/green color channels
-
add_marker
(x, y, color='k', markersize=10)[source]
Add marker to layer images.
-
add_polygon
()[source]
Add polygon to each image.
-
clear_markers
()[source]
” Remove all markers.
-
overlay
(msg, s=18)[source]
Overlay string centered on image.
-
remove_marker
()[source]
Remove marker from layer images.
-
remove_polygon
()[source]
Remove polygon from each image.
-
render_images
(layer, cmap=None)[source]
Add blue, green, and red channels of layer to axes.
Args:
layer (Layer) - RGB image layer
cmap (matplotlib.colors.ColorMap)
-
update_marker
(color, markersize, ind=-1)[source]
Update size and color of last added marker.
-
class
flyqma.selection.interface.
StackInterface
(stack)[source]
Object for visualizing multiple layers in an image stack.
Attributes:
path (str) - layer path
axes (array like) - axes for blue/red/green color channels
-
build_interface
(stack)[source]
Build interface by adding interface for each layer.
Args:
stack (Stack) - image stack
Event Handling
Tools for managing GUI-mediated event-handling.
-
class
flyqma.selection.gui.
GUI
(stack)[source]
GUI for manually selecting regions within each layer of an image stack.
Following instantiation, run “GUI.connect()” to begin event handling.
Key actions:
T: remove last added point
Y: reset all points in layer
E: exclude entire layer
W: save ROI data
Q: disconnect and exit GUI
-
connect
()[source]
Connect event handling.
-
disconnect
()[source]
Disconnect event handling.
-
exit
()[source]
Disconnect and exit GUI.
-
static
load
(stack)[source]
Load selection GUI from file.
Args:
stack (Stack) - image stack
Returns:
gui (GUI) - disconnected gui
-
on_click
(event)[source]
Click action: add point.
-
on_key
(event)[source]
Key actions.
T: remove last added point
Y: reset all points in layer
E: exclude entire layer
W: save ROI data
Q: disconnect and exit GUI
-
save
(image=True)[source]
Save selection path for each layer.
Args:
image (bool) - if True, save overall image of selections
-
which_layer
(event)[source]
Returns layer ID where event took place.