def test_config_cli_edit(conf_path):
runner = CliRunner()
runner.invoke(
config.cli_modify_config,
["edit", "-n", "z_board.read.min_val", "-v", "7", "-p", str(conf_path)],
)
conf = config.read_config(conf_path)
assert conf["z_board"]["read"]["min_val"] == 7
def _apply_config(self):
global conf
config_key = self.retrieve_keys_from_nested(
self.config_combo.currentText(), "-"
)
value = self._search_nested_dict(config_key, conf)
new_value = int(self.config_key_value.toPlainText())
new_value = type(value)(new_value) # Convert to keep the same type
write_config_value(config_key, new_value)
conf = read_config()
self.restart_lbl.show()
from sashimi.state import (
State,
get_voxel_size,
)
import napari
# TODO: In future realeases of napari remove monkey patched code. Accessing protected elements is bad practice
from napari.layers.shapes._shapes_constants import Mode
import numpy as np
from warnings import warn
from sashimi.hardware.cameras.interface import CameraWarning
from sashimi.config import read_config
from enum import Enum
from multiprocessing import Queue
conf = read_config()
class RoiState(Enum):
FULL = 1
DISPLAYED = 2
SET = 3
ROI_TEXTS = {
RoiState.FULL: "Select ROI",
RoiState.DISPLAYED: "Set ROI",
RoiState.SET: "Reset full frame",
}
def test_write_config_val(conf_path):
val = 6
config.write_config_value(["z_board", "read", "min_val"], val, file_path=conf_path)
conf = config.read_config(file_path=conf_path)
assert conf["z_board"]["read"]["min_val"] == val
def test_config_creation(conf_path):
conf = config.read_config(file_path=conf_path)
assert conf == config.TEMPLATE_CONF_DICT
def __init__(self, process_name):
self.file: Optional[TextIO] = None
self.process_name = process_name
configuration = config.read_config()
self.root = Path(configuration["default_paths"]["log"])
def __init__(self):
self.conf = read_config()
self.sample_rate = conf["sample_rate"]
self.logger = ConcurrenceLogger("main")
self.calibration_ref = None
self.waveform = None
self.current_plane = 0
self.stop_event = LoggedEvent(self.logger, SashimiEvents.CLOSE_ALL)
self.restart_event = LoggedEvent(self.logger,
SashimiEvents.RESTART_SCANNING)
self.experiment_start_event = LoggedEvent(
self.logger, SashimiEvents.SEND_EXT_TRIGGER)
self.noise_subtraction_active = LoggedEvent(
self.logger, SashimiEvents.NOISE_SUBTRACTION_ACTIVE, Event())
self.is_saving_event = LoggedEvent(self.logger,
SashimiEvents.IS_SAVING)
# The even active during scanning preparation (before first real camera trigger)
self.is_waiting_event = LoggedEvent(self.logger,
SashimiEvents.WAITING_FOR_TRIGGER)
self.experiment_state = ExperimentPrepareState.PREVIEW
self.status = ScanningSettings()
self.scanner = ScannerProcess(
stop_event=self.stop_event,
restart_event=self.restart_event,
waiting_event=self.is_waiting_event,
sample_rate=self.sample_rate,
)
self.camera_settings = CameraSettings()
self.trigger_settings = TriggerSettings()
self.settings_tree = ParameterTree()
self.pause_after = False
if self.conf["scopeless"]:
self.light_source = light_source_class_dict["mock"]()
else:
self.light_source = light_source_class_dict[
conf["light_source"]["name"]](
port=conf["light_source"]["port"])
self.camera = CameraProcess(
stop_event=self.stop_event,
wait_event=self.scanner.wait_signal,
exp_trigger_event=self.experiment_start_event,
)
self.multiprocessing_manager = MultiprocessingManager()
self.experiment_duration_queue = self.multiprocessing_manager.Queue()
self.external_comm = ExternalComm(
stop_event=self.stop_event,
experiment_start_event=self.experiment_start_event,
is_saving_event=self.is_saving_event,
is_waiting_event=self.is_waiting_event,
duration_queue=self.experiment_duration_queue,
)
self.saver = StackSaver(
stop_event=self.stop_event,
is_saving_event=self.is_saving_event,
duration_queue=self.experiment_duration_queue,
)
self.dispatcher = VolumeDispatcher(
stop_event=self.stop_event,
saving_signal=self.saver.saving_signal,
wait_signal=self.scanner.wait_signal,
noise_subtraction_on=self.noise_subtraction_active,
camera_queue=self.camera.image_queue,
saver_queue=self.saver.save_queue,
)
self.camera_settings = CameraSettings()
self.save_settings = SaveSettings()
self.settings_tree = ParameterTree()
self.global_state = GlobalState.PAUSED
self.planar_setting = PlanarScanningSettings()
self.light_source_settings = LightSourceSettings()
self.light_source_settings.params.intensity.unit = (
self.light_source.intensity_units)
self.save_status: Optional[SavingStatus] = None
self.single_plane_settings = SinglePlaneSettings()
self.volume_setting = ZRecordingSettings()
self.calibration = Calibration()
for setting in [
self.planar_setting,
self.light_source_settings,
self.single_plane_settings,
self.volume_setting,
self.calibration,
self.calibration.z_settings,
self.camera_settings,
self.save_settings,
]:
self.settings_tree.add(setting)
self.status.sig_param_changed.connect(self.change_global_state)
self.planar_setting.sig_param_changed.connect(
self.send_scansave_settings)
self.calibration.z_settings.sig_param_changed.connect(
self.send_scan_settings)
self.single_plane_settings.sig_param_changed.connect(
self.send_scan_settings)
self.volume_setting.sig_param_changed.connect(self.send_scan_settings)
self.save_settings.sig_param_changed.connect(
self.send_scansave_settings)
self.camera.start()
self.scanner.start()
self.external_comm.start()
self.saver.start()
self.dispatcher.start()
self.current_binning = conf["camera"]["default_binning"]
self.send_scansave_settings()
self.logger.log_message("initialized")
self.voxel_size = None
