def save_outputs_dcm_overlay(self):
# TODO add
logger.debug('save dcm')
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
# mport ipdb; ipdb.set_trace() # BREAKPOINT
odp = self.output_datapath
pth, filename = op.split(op.normpath(self.datapath))
filename += "-" + self.experiment_caption
# f savestring in ['ad']:
# save to DICOM
filepath = 'dicom-' + filename
filepath = os.path.join(odp, filepath)
filepath = misc.suggest_filename(filepath)
output_dicom_dir = filepath
data = self.export()
# mport ipdb; ipdb.set_trace() # BREAKPOINT
overlays = {
3:
(data['segmentation'] == self.output_label).astype(np.int8)
}
if self.dcmfilelist is not None:
datawriter.saveOverlayToDicomCopy(
self.dcmfilelist,
output_dicom_dir, overlays,
data['crinfo'], data['orig_shape'])
def main():
pyqtRemoveInputHook()
QDir(QDir.homePath()).mkdir(".ricodebug")
app = QApplication(sys.argv)
app.setApplicationName("ricodebug")
Icons()
# We use all kinds of loggers here:
# * a CriticalLogHandler that will abort the program whenever a critical error is received
# * a FileHandler writing to a log in the home directory (all messages, for debugging)
# * a LogViewHandler to have the log available in the GUI
# * a ErrorLabelHandler that visually notifies the user of an error or a warning
logger = logging.getLogger()
formatter = logging.Formatter('[%(levelname)-8s] : %(filename)15s:%(lineno)4d/%(funcName)-20s : %(message)s')
filehandler = logging.FileHandler(filename='%s/.ricodebug/ricodebug.log' % str(QDir.homePath()))
filehandler.setFormatter(formatter)
logger.addHandler(filehandler)
logger.setLevel(logging.DEBUG)
logger.addHandler(criticalloghandler.CriticalLogHandler())
window = MainWindow()
logger.addHandler(window.logviewhandler)
logger.addHandler(window.notificationFrameHandler)
if (len(sys.argv) > 1):
window.debugController.openExecutable(sys.argv[1])
window.show()
logging.shutdown()
sys.exit(app.exec_())
def debug_trace():
# Sets a tracepoint in the Python debugger that works with Qt
from PyQt4.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()
def info(type, value, tb):
from PyQt4.QtCore import pyqtRemoveInputHook
for line in traceback.format_exception(type, value, tb):
sys.stdout.write(line)
pyqtRemoveInputHook()
from pdb import pm
pm()
def set_trace():
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
import pdb
pdb.Pdb().set_trace(sys._getframe().f_back)
def debug_after(*args, **kwargs):
try:
return func(*args, **kwargs)
except Exception,e:
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
import pdb;pdb.set_trace()
def debug_trace(break_to = "ipy", use_globals = True):
""" Set a tracepoint in the Python debugger that works with Qt (tested
on pyqt and pyside 1.0.7)
"""
from PyQt4.QtCore import pyqtRemoveInputHook
from IPython import embed
from pdb import set_trace
# Get the locals and globals dict from the location where this function
# was called.
import sys
previous_frame = sys._getframe(1)
l = previous_frame.f_locals
if use_globals:
g = previous_frame.f_globals
namespace = g
else:
namespace = {}
namespace.update(l)
# Stop the QT check for gui event loop and put the break point
pyqtRemoveInputHook()
if break_to == "ipy":
embed(user_ns=namespace)
else:
set_trace()
def _rls_to_pyd(r_ls):
# base case is that the type is a native python type, rather
# than an Rvector
d = {}
for name, val in zip(r_ls.getnames(), r_ls):
try:
# first check the key
if str(name) != "NULL":
print name
print type(name)
if "rpy2.robjects" in str(type(name)):
name = str(name[0])
if not "rpy2.robjects" in str(type(val)):
# base case; not an rtype object
d[name] = val
elif str(val)=="NULL":
d[name] = None
elif str(val.getnames())=="NULL":
d[name] = val[0]
else:
d[name] = _rls_to_pyd(val)
if not isinstance(name, str):
raise Exception, "arg"
else:
# name is null
return val
except Exception, inst:
print inst
pyqtRemoveInputHook()
pdb.set_trace()
def fout(*args,**kwargs):
logger.info('Temporarily disabling figure interactivity')
pyqtRemoveInputHook()
out = fin(*args,**kwargs)
pyqtRestoreInputHook()
logger.info('Figure interactivity has been restored')
return out
def dev_mode(back):
# Help -> Developer Help
steal_again = back.front.return_stdout()
hs = back.hs # NOQA
front = back.front
wasBlocked = front.blockSignals(True)
devmode = True # NOQA
print(helpers.indent(str(hs), '[*back.hs] '))
rrr()
print(r'[\back] finished dev_help')
#app = back.app
#from PyQt4 import QtGui
#QtGui.qApp.quit()
#app.exit() # Stop the main loop
#app.quit()
#if back.timer is not None:
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
#from IPython.lib.inputhook import enable_qt4
#enable_qt4()
execstr = helpers.ipython_execstr()
#print(execstr)
print('Debugging in IPython. IPython will break gui until you exit')
exec(execstr)
if steal_again:
back.front.steal_stdout()
back.front.blockSignals(wasBlocked)
def debug_trace():
'''Set a tracepoint in the Python debugger that works with Qt'''
if pyqt:
from PyQt4.QtCore import pyqtRemoveInputHook
from pdb import set_trace
if pyqt:
pyqtRemoveInputHook()
set_trace()
def pdb(debug=False):
print traceback.print_exc()
if debug:
from PyQt4.QtCore import pyqtRemoveInputHook
import pdb
pyqtRemoveInputHook()
pdb.set_trace()
def debug_trace(trigger=False):
'''Set a tracepoint in the Python debugger that works with Qt'''
if trigger:
return
from PyQt4.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()
def debug_trace():
"""
Set a tracepoint in the Python debugger that works with Qt
:return: None
"""
from PyQt4.QtCore import pyqtRemoveInputHook
#from pdb import set_trace
pyqtRemoveInputHook()
def debug_trace(self, *args):
'''Set a tracepoint in the Python debugger that works with Qt'''
try:
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
except ImportError:
pass
self.set_trace(sys._getframe().f_back)
def main():
pyqtRemoveInputHook()
os.environ['LANG'] = "en_EN.UTF-8"
app = QtGui.QApplication(sys.argv)
app.setStyle('Windows') # 'Windows', 'Motif', 'CDE',
# 'Plastique', 'GTK+', 'Cleanlooks'
mainform = MainForm(app)
mainform.show()
app.exec_()
def _enable_pdb(): # pragma: no cover
from IPython.core import ultratb
logger.debug("Enabling debugger.")
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
sys.excepthook = ultratb.FormattedTB(mode='Verbose',
color_scheme='Linux',
call_pdb=True,
)
def pyqt_set_trace():
pyqtRemoveInputHook()
debugger = pdb.Pdb()
debugger.reset()
debugger.do_next(None)
users_frame = sys._getframe().f_back
debugger.interaction(users_frame, None)
def set_trace():
pyqtRemoveInputHook()
# set up the debugger
debugger = pdb.Pdb()
debugger.reset()
# custom next to get outside of function scope
debugger.do_next(None) # run the next command
users_frame = sys._getframe().f_back # frame where the user invoked `pyqt_set_trace()`
debugger.interaction(users_frame, None)
def debug_trace():
"""Set a tracepoint in the Python debugger that works with Qt."""
if py_binding == 'PyQt4':
from PyQt4.QtCore import pyqtRemoveInputHook
elif py_binding == 'PySide':
from PySide.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()
def get_display_effect(self, effect, group_str):
try:
if "display_est" in self.effects_dict[effect][group_str]:
return self.effects_dict[effect][group_str]["display_est"]
else:
return None
except:
pyqtRemoveInputHook()
pdb.set_trace()
def create_widget():
argv = sys.argv
pyqtRemoveInputHook()
window = IPythonWidget()
window.embed_ipython()
window.show()
return window
def run_debug(self, event):
"""
Stop processing and start debugger in console. Function started by
pressing "Debug" button wich is availeble after starting Lisa with
-d parameter.
"""
logger.debug('== Starting debug mode, leave it with command "c" =')
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
import ipdb; ipdb.set_trace() # noqa BREAKPOINT
def ipdb_set_trace():
'''ipdb version'''
try:
import ipdb
except ImportError:
pass
else:
pyqtRemoveInputHook()
ipdb.set_trace(sys._getframe(1))
pyqtRestoreInputHook()
def qt4_pdb(ipython=True):
'''Set a tracepoint in the Python debugger that works with Qt'''
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
if ipython:
from IPython.core.debugger import Tracer
return Tracer(colors='Linux')
else:
from pdb import set_trace
return set_trace
def get_config_as_dict(self):
dictionary = self.config.as_dict()
for key, value in dictionary.iteritems():
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
if type(value) == PyQt4.QtCore.QString:
value = str(value)
dictionary[key] = value
return dictionary
def pyqt_trace():
'''Set a tracepoint in the Python debugger that works with Qt'''
from PyQt4.QtCore import pyqtRemoveInputHook
import pdb
import sys
pyqtRemoveInputHook()
# set up the debugger
debugger = pdb.Pdb()
debugger.reset()
# custom next to get outside of function scope
debugger.do_next(None) # run the next command
users_frame = sys._getframe().f_back # frame where the user invoked `pyqt_set_trace()`
debugger.interaction(users_frame, None)
def main():
pyqtRemoveInputHook()
QDir(QDir.homePath()).mkdir(".ricodebug")
app = QApplication(sys.argv)
app.setApplicationName("ricodebug")
window = None
Logger.getInstance().init("logfile", window)
window = MainWindow()
if (len(sys.argv) > 1):
window.debug_controller.openExecutable(sys.argv[1])
window.show()
sys.exit(app.exec_())
def set_trace(frame=None):
'''
Set a tracepoint in the Python debugger that works with Qt
Taken from:
http://stackoverflow.com/questions/1736015/debugging-a-pyqt4-app
'''
from PyQt4.QtCore import pyqtRemoveInputHook
try:
from ipdb import set_trace
except ImportError:
from pdb import set_trace
pyqtRemoveInputHook()
if frame is None:
frame = sys._getframe().f_back
return set_trace(frame)
def debug_start():
'''pdb.set_trace wrapper
Notes
-----
Basically to handle Qt debugging. This allows
Qt apps to be debugged without issue with the
event loop.
Simply use this function instead of pdb.set_trace()
But, also see debug_stop.
'''
from pdb import set_trace
try:
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
except NameError:
pass
set_trace()
def debug():
from PyQt4.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()
def debug_trace():
'''Set a tracepoint in the Python debugger that works with Qt'''
from PyQt4.QtCore import pyqtRemoveInputHook
from pdb import set_trace
pyqtRemoveInputHook()
set_trace()
def pdb(locals):
pyqtRemoveInputHook()
import pdb
pdb.set_trace()
