def runModule(module_type, setup_name = False):
app = QtGui.QApplication(sys.argv)
general_parameters = params.halParameters("settings_default.xml")
if setup_name:
general_parameters.set("setup_name", setup_name)
else:
setup_name = general_parameters.get("setup_name")
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
found = False
for module in hardware.get("modules").getProps():
if (module.get("hal_type") == module_type):
a_module = __import__(module.get("module_name"), globals(), locals(), [setup_name], -1)
a_class = getattr(a_module, module.get("class_name"))
instance = a_class(module.get("parameters", False), general_parameters, None)
params.setDefaultParameters(general_parameters)
setup_parameters = params.halParameters("xml/" + setup_name + "_default.xml")
instance.newParameters(setup_parameters)
instance.show()
found = True
break
if found:
app.exec_()
instance.cleanup()
else:
print module_type, "not found for", setup_name, "setup"
def runModule(module_type, setup_name = False):
app = QtGui.QApplication(sys.argv)
parameters = params.parameters("settings_default.xml")
if not setup_name:
setup_name = parameters.get("setup_name")
parameters = params.halParameters("xml/" + setup_name + "_default.xml")
parameters.set("setup_name", setup_name)
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
found = False
for module in hardware.modules:
if (module.hal_type == module_type):
a_module = __import__(module.module_name, globals(), locals(), [setup_name], -1)
a_class = getattr(a_module, module.class_name)
instance = a_class(module.parameters, parameters, None)
instance.newParameters(parameters)
instance.show()
found = True
break
if found:
app.exec_()
instance.cleanup()
else:
print module_type, "not found for", setup_name, "setup"
def runModule(module_type, setup_name = False):
app = QtGui.QApplication(sys.argv)
parameters = params.parameters("settings_default.xml")
if not setup_name:
setup_name = parameters.get("setup_name")
parameters = params.halParameters("xml/" + setup_name + "_default.xml")
parameters.set("setup_name", setup_name)
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
found = False
for module in hardware.get("modules").getSubXMLObjects():
if (module.get("hal_type") == module_type):
a_module = __import__(module.get("module_name"), globals(), locals(), [setup_name], -1)
a_class = getattr(a_module, module.get("class_name"))
instance = a_class(module.get("parameters", False), parameters, None)
instance.newParameters(parameters)
instance.show()
found = True
break
if found:
app.exec_()
instance.cleanup()
else:
print module_type, "not found for", setup_name, "setup"
def newSettings(self, parameters_filename):
# parse parameters file
is_valid_xml = True
try:
parameters = params.halParameters(parameters_filename)
except params.ParametersException:
is_valid_xml = False
hdebug.logText("failed to parse parameters file " + parameters_filename)
QtGui.QMessageBox.information(self, "Parameter file parsing error", traceback.format_exc())
if is_valid_xml:
self.parameters_box.addParameters(parameters)
def newSettings(self, parameters_filename):
# parse parameters file
is_valid_xml = True
try:
parameters = params.halParameters(parameters_filename)
except params.ParametersException:
is_valid_xml = False
hdebug.logText("failed to parse parameters file " +
parameters_filename)
QtGui.QMessageBox.information(self, "Parameter file parsing error",
traceback.format_exc())
if is_valid_xml:
self.parameters_box.addParameters(parameters)
import camera.frame as frame
# This file is available in the ZhuangLab storm-analysis project on github.
import sa_library.datareader as datareader
if (len(sys.argv) != 4):
print "usage: <settings> <movie_in> <png_out>"
exit()
# Open movie & get size.
data_file = datareader.inferReader(sys.argv[2])
[width, height, length] = data_file.filmSize()
# Start spotCounter as a stand-alone application.
app = QtGui.QApplication(sys.argv)
parameters = params.halParameters(sys.argv[1])
parameters.set("setup_name", "offline")
parameters.set("camera1.x_pixels", width)
parameters.set("camera1.y_pixels", height)
parameters.set("camera1.x_bin", 1)
parameters.set("camera1.y_bin", 1)
spotCounter = SingleSpotCounter(None, parameters)
#spotCounter.newParameters(parameters, [[255,255,255]])
spotCounter.newParameters(parameters)
# Start driver.
driver = OfflineDriver(spotCounter, data_file, sys.argv[3])
# Show window & start application.
if (sys.platform == "linux2"):
font = QtGui.QFont()
font.setPointSize(8)
app.setFont(font)
# Splash Screen.
pixmap = QtGui.QPixmap("splash.png")
splash = QtGui.QSplashScreen(pixmap)
splash.show()
app.processEvents()
# Load settings.
if (len(sys.argv) == 4):
setup_name = sys.argv[1]
hardware = params.hardware(sys.argv[2])
parameters = params.halParameters(sys.argv[3])
else:
parameters = params.parameters("settings_default.xml")
setup_name = parameters.get("setup_name")
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
parameters = params.halParameters("xml/" + setup_name + "_default.xml")
params.setSetupName(parameters, setup_name)
# Start logger.
hdebug.startLogging(parameters.get("film.directory") + "logs/", "hal4000")
# Load app.
window = Window(hardware, parameters)
window.toggleSettings()
splash.hide()
window.show()
if __name__ == "__main__":
app = QtGui.QApplication(sys.argv)
# Splash Screen.
pixmap = QtGui.QPixmap("splash.png")
splash = QtGui.QSplashScreen(pixmap)
splash.show()
app.processEvents()
# Load settings.
if (len(sys.argv) == 4):
setup_name = sys.argv[1]
hardware = params.hardware(sys.argv[2])
parameters = params.halParameters(sys.argv[3])
else:
parameters = params.parameters("settings_default.xml")
setup_name = parameters.get("setup_name")
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
parameters = params.halParameters("xml/" + setup_name + "_default.xml")
params.setSetupName(parameters, setup_name)
# Start logger.
hdebug.startLogging(parameters.get("film.directory") + "logs/", "hal4000")
# Load app.
window = Window(hardware, parameters)
window.toggleSettings()
splash.hide()
window.show()
import camera.frame as frame
# This file is available in the ZhuangLab storm-analysis project on github.
import sa_library.datareader as datareader
if (len(sys.argv) != 4):
print "usage: <settings> <movie_in> <png_out>"
exit()
# Open movie & get size.
data_file = datareader.inferReader(sys.argv[2])
[width, height, length] = data_file.filmSize()
# Start spotCounter as a stand-alone application.
app = QtGui.QApplication(sys.argv)
parameters = params.halParameters(sys.argv[1])
parameters.set("setup_name", "offline")
parameters.set("camera1.x_pixels", width)
parameters.set("camera1.y_pixels", height)
parameters.set("camera1.x_bin", 1)
parameters.set("camera1.y_bin", 1)
spotCounter = SingleSpotCounter(None, parameters)
spotCounter.newParameters(parameters)
# Set the color.
#
# FIXME: We should parse the shutters file listed in the parameters
# file. However instead we just use white.
#
app = QtGui.QApplication(sys.argv)
# Set default font size for linux.
if (sys.platform == "linux2"):
font = QtGui.QFont()
font.setPointSize(8)
app.setFont(font)
# Splash Screen.
pixmap = QtGui.QPixmap("splash.png")
splash = QtGui.QSplashScreen(pixmap)
splash.show()
app.processEvents()
# Load general settings.
general_parameters = params.halParameters("settings_default.xml")
# Load setup specific settings, just to get access to the
# setup name and the film (and logging) directory.
if (len(sys.argv) == 4):
setup_name = sys.argv[1]
hardware = params.hardware(sys.argv[2])
setup_parameters_filename = sys.argv[3]
else:
setup_name = general_parameters.get("setup_name")
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
setup_parameters_filename = "xml/" + setup_name + "_default.xml"
setup_parameters = params.parameters(setup_parameters_filename, True)
# Update general parameters with specific settings that are needed at startup.
app = QtGui.QApplication(sys.argv)
# Set default font size for linux.
if (sys.platform == "linux2"):
font = QtGui.QFont()
font.setPointSize(8)
app.setFont(font)
# Splash Screen.
pixmap = QtGui.QPixmap("splash.png")
splash = QtGui.QSplashScreen(pixmap)
splash.show()
app.processEvents()
# Load general settings.
general_parameters = params.halParameters("settings_default.xml")
# Load setup specific settings, just to get access to the
# setup name and the film (and logging) directory.
if (len(sys.argv) == 4):
setup_name = sys.argv[1]
hardware = params.hardware(sys.argv[2])
setup_parameters_filename = sys.argv[3]
else:
setup_name = general_parameters.get("setup_name")
hardware = params.hardware("xml/" + setup_name + "_hardware.xml")
setup_parameters_filename = "xml/" + setup_name + "_default.xml"
setup_parameters = params.parameters(setup_parameters_filename, True)
# Update general parameters with specific settings that are needed at startup.