def start_cube_extraction(viewer):
"""Extract cubes for training"""
if not output_filename.exists():
print("No curation results have been saved. "
"Please save before extracting cubes")
else:
print(f"Saving cubes to: {output_directory}")
run_extraction(
output_filename,
output_directory,
args.signal_image_paths,
args.background_image_paths,
args.cube_depth,
args.cube_width,
args.cube_height,
args.x_pixel_um,
args.y_pixel_um,
args.z_pixel_um,
args.x_pixel_um_network,
args.y_pixel_um_network,
args.z_pixel_um_network,
args.max_ram,
args.n_free_cpus,
args.save_empty_cubes,
)
print("Saving yaml file to use for training")
save_yaml_file(output_directory)
print("Closing window")
QApplication.closeAllWindows()
print("Finished! You may now annotate more "
"datasets, or go straight to training")
def powrot(self):
self.window = QtWidgets.QMainWindow()
self.ui = main.Ui_MainWindow()
self.ui.setupUi(self.window)
QApplication.closeAllWindows()
self.qt2_app = oknoAdmin.App()
self.qt2_app.show()
def close(self) -> None:
try:
self.stop_music()
QApplication.closeAllWindows()
except Exception as e:
sys.exit(1)
if DEBUG: print(e)
else:
print('App closed')
def testQPushButtonQLabel(self):
button = QPushButton()
label = QLabel()
button.pressed.connect(lambda: label.setText("Hello!"))
self.assertTrue(label.text() == '')
QTest.mouseClick(button, Qt.LeftButton)
self.assertTrue(label.text() == "Hello!")
QApplication.closeAllWindows()
def testQPushButton(self):
button = QPushButton()
button.setCheckable(True)
button.setChecked(False)
QTest.mouseClick(button, Qt.LeftButton)
self.assertTrue(button.isChecked())
QTest.mouseClick(button, Qt.LeftButton)
self.assertFalse(button.isChecked())
QApplication.closeAllWindows()
def conv_to_b(v):
selected_points = v.layers[-1].selected_data
if len(selected_points) == 1:
print(f"labeled point at {v.layers[-1].data}")
z = int(v.layers[-1].data[0][0])
y = int(v.layers[-1].data[0][1])
x = int(v.layers[-1].data[0][2])
seed_point = (x, y, z)
seed_point_str = f"{x}_{y}_{z}"
print(f"{seed_point} extracted, getting fiber track from this")
get_fiber_track(
reg_dir / atlas_name,
reg_dir / background_channel_name,
seed_point,
reg_dir / output_name.format(seed_point_str),
)
print("closing application...")
QApplication.closeAllWindows()
class QtFrontend(ViewSBFrontend):
""" Qt Frontend that consumes packets for display. """
UI_NAME = 'qt'
UI_DESCRIPTION = 'unstable GUI in Qt'
# So, Qt's tree widgets require that column 0 have the expand arrow, but you _can_ change
# where column 0 is displayed.
# We want the summary column to have the expand arrow, so we'll swap it
# with the timestamp column in __init__().
COLUMN_TIMESTAMP = 5
COLUMN_DEVICE = 1
COLUMN_ENDPOINT = 2
COLUMN_DIRECTION = 3
COLUMN_LENGTH = 4
COLUMN_SUMMARY = 0
COLUMN_STATUS = 6
COLUMN_DATA = 7
@staticmethod
def reason_to_be_disabled():
try:
import PySide2
except ImportError:
return "PySide2 (Qt library) not available."
return None
@staticmethod
def _stringify_list(lst):
"""
Tiny helper than runs the str constructor on every item in a list, but specifically handles two cases:
1) the object in question is None, which we instead want to display as an empty string,
2) the resulting string contains a null character, which Qt doesn't like, so we'll
represent it to the user as, literally, \0.
"""
return [
str(x).replace('\0', r'\0') if x is not None else '' for x in lst
]
def _create_item_for_packet(self, viewsb_packet):
""" Creates a QTreeWidgetItem for a given ViewSBPacket.
Args:
viewsb_packet -- The ViewSBPacket to create the QTreeWidgetItem from.
Returns a QTreeWidgetItem.
"""
def get_packet_string_array(viewsb_packet):
""" Tiny helper to return and stringify the common fields used for the columns of tree items. """
direction = viewsb_packet.direction.name if viewsb_packet.direction is not None else ''
length = len(
viewsb_packet.data) if viewsb_packet.data is not None else ''
return self._stringify_list([
viewsb_packet.summarize(), viewsb_packet.device_address,
viewsb_packet.endpoint_number, direction, length,
viewsb_packet.timestamp,
viewsb_packet.summarize_status(),
viewsb_packet.summarize_data()
]) + [viewsb_packet]
item = QTreeWidgetItem(get_packet_string_array(viewsb_packet))
# Give the item a reference to the original packet object.
item.setData(0, QtCore.Qt.UserRole, viewsb_packet)
return item
def _recursively_walk_packet(self, viewsb_packet):
""" Recursively walks packet subordinates, batching QTreeWidgetItem.addChildren as much as possible.
Args:
viewsb_packet -- The top-level packet (as far as the caller's context is concerned).
"""
packet_item = self._create_item_for_packet(viewsb_packet)
packet_children_list = []
for sub_packet in viewsb_packet.subordinate_packets:
# Create the item for this packet, and recursively fill its children.
packet_children_list.append(
self._recursively_walk_packet(sub_packet))
packet_item.addChildren(packet_children_list)
return packet_item
def __init__(self):
""" Sets up the Qt UI. """
QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts)
signal.signal(
signal.SIGINT,
signal.SIG_DFL) # fix SIGINT handling - cleanly exit on ctrl+c
self.app = QApplication([])
self.ui_file = QtCore.QFile(
os.path.dirname(os.path.realpath(__file__)) + '/qt.ui')
self.loader = QUiLoader()
self.loader.registerCustomWidget(ViewSBQTreeWidget)
self.loader.registerCustomWidget(ViewSBHexView)
self.window = self.loader.load(self.ui_file) # type: QMainWindow
# Swap columns 0 and 5 to put the expand arrow on the summary column.
self.window.usb_tree_widget.header().swapSections(0, 5)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_TIMESTAMP, 120)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_DEVICE, 32)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_ENDPOINT, 24)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_DIRECTION, 42)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_LENGTH, 60)
self.window.usb_tree_widget.setColumnWidth(self.COLUMN_SUMMARY, 500)
self.window.update_timer = QtCore.QTimer()
self.window.update_timer.timeout.connect(self._update)
self.window.usb_tree_widget.currentItemChanged.connect(
self._tree_current_item_changed)
self.window.usb_tree_widget = self.window.usb_tree_widget
self.window.usb_tree_widget.sortByColumn(0)
self.window.showMaximized()
def _update(self):
""" Called by the QTimer `update_timer`; collects packets the queue and adds them to the tree view.
We use this instead of calling `handle_communications` and defining `handle_incoming_packet`,
because adding items one at a time as we receive them is slower than batching them.
Note: Since this is called via a QTimer signal, this method runs in the UI thread.
"""
# If the process manager told us to stop (which might happen if e.g. the backend exits),
# then stop and exit.
if self.termination_event.is_set():
self.app.closeAllWindows()
packet_list = []
try:
# Get as many packets as we can as quick as we can.
while True:
packet = self.data_queue.get_nowait()
packet_list.append(packet)
# But the instant it's empty, don't wait for any more; just send them to be processed.
except multiprocessing.queues.Empty:
pass
finally:
self.add_packets(packet_list)
def _tree_current_item_changed(self, current_item, _previous_item):
"""
Handler for the QTreeWidget.currentItemChanged() signal that populates the side panels with
detail fields and a hex representation of the current packet.
"""
# Clear the details widget.
self.window.usb_details_tree_widget.clear()
current_packet = current_item.data(0, QtCore.Qt.UserRole)
# A list of 2-tuples: first element is a table title, and the second is usually a string:string dict.
detail_fields = current_packet.get_detail_fields()
if detail_fields:
self.update_detail_fields(detail_fields)
self.window.usb_hex_view.populate(current_packet.get_raw_data())
def update_detail_fields(self, detail_fields):
""" Populates the detail view with the relevant fields for the selected packet. """
# Each table will have a root item in the details view.
root_items = []
for table in detail_fields:
title = table[0]
root = QTreeWidgetItem([title])
children = []
fields = table[1]
# The usual case: a str:str dict.
if isinstance(fields, dict):
for key, value in fields.items():
children.append(
QTreeWidgetItem(self._stringify_list([key, value])))
# Sometimes it'll just be a 1-column list.
elif isinstance(fields, list):
for item in fields:
children.append(
QTreeWidgetItem(self._stringify_list([item])))
# Sometimes it'll just be a string, or a `bytes` instance.
else:
children.append(QTreeWidgetItem(self._stringify_list([fields
])))
root.addChildren(children)
# Add an empty "item" between each table.
root_items.extend([root, QTreeWidgetItem([])])
self.window.usb_details_tree_widget.addTopLevelItems(root_items)
self.window.usb_details_tree_widget.expandAll()
self.window.usb_details_tree_widget.resizeColumnToContents(0)
self.window.usb_details_tree_widget.resizeColumnToContents(1)
def add_packets(self, viewsb_packets):
""" Adds a list of top-level ViewSB packets to the tree.
We're in the UI thread; every bit of overhead counts, so let's batch as much as possible.
"""
top_level_items_list = []
for viewsb_packet in viewsb_packets:
# Create the item for this packet, and recursively fill its children.
top_level_items_list.append(
self._recursively_walk_packet(viewsb_packet))
self.window.usb_tree_widget.addTopLevelItems(top_level_items_list)
def run(self):
""" Overrides ViewSBFrontend.run(). """
# TODO: is there a better value than 100 ms? Should it be configurable by the Analyzer?
self.window.update_timer.start(100)
self.app.exec_()
self.stop()
def stop(self):
self.app.closeAllWindows()
self.termination_event.set()
def close_viewer(viewer):
print("\nClosing viewer")
QApplication.closeAllWindows()
def quit(v):
QApplication.closeAllWindows()
class QtFrontend(ViewSBFrontend):
""" Qt Frontend that consumes packets for display. """
UI_NAME = 'qt'
UI_DESCRIPTION = 'proof-of-concept, unstable GUI in Qt'
@staticmethod
def reason_to_be_disabled():
# If we weren't able to import pyside2, disable the library.
if 'QWidget' not in globals():
return "pyside2 (qt library) not available"
return None
def __init__(self):
""" Sets up the Qt UI. """
QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts)
self.app = QApplication([])
self.ui_file = QtCore.QFile('viewsb/frontends/qt.ui')
self.loader = QUiLoader()
self.window: QtWidgets.QMainWindow = self.loader.load(self.ui_file)
# The default column size of 100 is too small for the summary column.
self.window.usb_tree_widget.setColumnWidth(1, 400)
self.window.update_timer = QtCore.QTimer()
self.window.update_timer.timeout.connect(self.update)
self.window.usb_tree_widget.currentItemChanged.connect(
self.tree_current_item_changed)
self.window.usb_tree_widget: QtWidgets.QTreeWidget = self.window.usb_tree_widget
self.window.usb_tree_widget.sortByColumn(0)
self.window.showMaximized()
def update(self):
""" Called by the QTimer `update_timer`, collects packets waiting the queue and adds them to the tree view.
Note: Since this is called via a QTimer signal, this method runs in the UI thread.
"""
packet_list = []
try:
# Get as many packets as we can as quick as we can.
while (True):
packet = self.data_queue.get_nowait()
packet_list.append(packet)
# But the instant it's empty, don't wait for any more; just send them to be processed.
except multiprocessing.queues.Empty:
pass
finally:
# In case the queue was empty in the first place and didn't have anything ready.
if len(packet_list) > 0:
self.add_packets(packet_list)
def add_packets(self, viewsb_packets: []):
""" Adds a list of top-level ViewSB packets to the tree.
We're in the UI thread; every bit of overhead counts, so let's batch as much as possible.
"""
for viewsb_packet in viewsb_packets:
top_level_item = QtWidgets.QTreeWidgetItem(
get_packet_string_array(viewsb_packet))
top_level_item.setData(0, QtCore.Qt.UserRole, viewsb_packet)
list_of_children = []
recursive_packet_walk(viewsb_packet, list_of_children)
top_level_item.addChildren(list_of_children)
self.window.usb_tree_widget.addTopLevelItem(top_level_item)
def tree_current_item_changed(self, current_item, previous_item):
""" Use the side panel to show a detailed view of the current item. """
# Clear the details widget.
self.window.usb_details_tree_widget.clear()
self.window.usb_details_tree_widget.setColumnCount(2)
current_packet: ViewSBPacket = current_item.data(0, QtCore.Qt.UserRole)
# A list of 2-tuples: first element is a table title, and the second is usually a string: string dict
detail_fields = current_packet.get_detail_fields()
# Each table will have a root item in the details view.
root_items = []
for table in detail_fields:
title: str = table[0]
root = QtWidgets.QTreeWidgetItem([title])
children = []
fields = table[1]
# The usual case: a str: str dict.
if type(fields) == type({}):
for key, value in fields.items():
children.append(
QtWidgets.QTreeWidgetItem(stringify_list([key,
value])))
# Sometimes a descriptor will just be a 1-column list.
elif type(fields) == type([]):
for item in fields:
children.append(QtWidgets.QTreeWidgetItem([str(item)]))
# Sometimes it'll just be a string, or, if it's an unknown descriptor, a `bytes` instance.
else:
children.append(QtWidgets.QTreeWidgetItem([str(fields)]))
root.addChildren(children)
# Add an empty "item" between each table
root_items += [root, QtWidgets.QTreeWidgetItem([])]
self.window.usb_details_tree_widget.addTopLevelItems(root_items)
self.window.usb_details_tree_widget.expandAll()
self.window.usb_details_tree_widget.resizeColumnToContents(0)
self.window.usb_details_tree_widget.resizeColumnToContents(1)
def run(self):
""" Overrides `ViewSBFrontend.run()` """
# TODO: is there a better value than 100 ms? Should it be configurable by the Analyzer?
self.window.update_timer.start(100)
self.app.exec_()
self.stop()
def stop(self):
self.app.closeAllWindows()
self.termination_event.set()
