class RespirationCycleEdition(QDialog):
"""
"""
def __init__(
self,
parent=None,
metadata=None,
Session=None,
session=None,
globalApplicationDict=None,
id_respirationsignal=None,
):
QDialog.__init__(self, parent)
self.metadata = metadata
self.session = Session()
self.globalApplicationDict = globalApplicationDict
self.id_respirationsignal = id_respirationsignal
self.respiration = self.session.query(RespirationSignal).filter_by(
id=id_respirationsignal).one()
#FIXME: do not work:
self.setModal(False)
self.setWindowModality(Qt.NonModal)
self.setWindowTitle(
self.tr('OpenElectrophy respiration for %d' %
(self.respiration.id)))
self.setWindowIcon(QIcon(':/respiration.png'))
self.mainLayout = QVBoxLayout()
self.setLayout(self.mainLayout)
h = QHBoxLayout()
self.mainLayout.addLayout(h)
c = SimpleCanvasAndTool()
h.addWidget(c, 3)
self.canvas = c.canvas
self.ax = self.canvas.fig.add_subplot(1, 1, 1)
v = QVBoxLayout()
h.addLayout(v, 2)
but = QPushButton(QIcon(':/TODO.txt'), 'Auto detect')
v.addWidget(but)
self.connect(but, SIGNAL('clicked()'), self.newDetection)
v.addSpacing(20)
v.addWidget(QLabel('<b>Repiratory cycles</b>'))
self.table = QTreeWidget()
#~ self.table.setMinimumWidth(100)
#~ self.table.setColumnWidth(0,80)
v.addWidget(self.table)
self.table.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.connect(self.table, SIGNAL('itemSelectionChanged()'),
self.newSelectionInTable)
self.table.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self.table,
SIGNAL('customContextMenuRequested( const QPoint &)'),
self.contextMenuTable)
self.mainLayout.addSpacing(20)
buttonBox = QDialogButtonBox()
but = QPushButton(QIcon(':/document-save.png'), 'Save to DB')
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.save_to_db)
but = QPushButton(QIcon(':/reload.png'), 'Reload from DB')
buttonBox.addButton(but, QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.reload_from_db)
but = QPushButton(QIcon(':/window-close.png'), 'Quit')
buttonBox.addButton(but, QDialogButtonBox.RejectRole)
self.connect(but, SIGNAL('clicked()'), self.close)
self.mainLayout.addWidget(buttonBox)
if self.respiration.cycle_times is None:
self.cycle_times = None
else:
self.cycle_times = self.respiration.cycle_times
self.vlines = {}
self.baseline = 0.
self.refreshPlot()
self.refreshTable()
self.canvas.mpl_connect('pick_event', self.onPick)
self.canvas.mpl_connect('button_release_event', self.releaseEvent)
self.canvas.mpl_connect('motion_notify_event', self.motionEvent)
#~ self.picked = None
#~ self.lineSelection = None
self.session.expunge_all()
def refreshPlot(self, with_same_zoom=False):
if with_same_zoom:
if self.canvas.toolbar._views.empty():
self.canvas.toolbar.push_current()
#~ self.canvas.toolbar.push_current()
xlim = self.ax.get_xlim()
ylim = self.ax.get_ylim()
self.ax.clear()
t = self.respiration.t()
sig = self.respiration.signal
self.ax.plot(t, sig, 'b')
if self.cycle_times is not None:
self.vlines = {}
cmap = get_cmap('jet', self.cycle_times.shape[0])
for i in range(self.cycle_times.shape[0]):
for j in range(self.cycle_times.shape[1]):
if j == 0: ls = '-'
else: ls = '--'
line = self.ax.axvline(self.cycle_times[i, j],
color=cmap(i),
linestyle=ls,
picker=3,
linewidth=1.5)
self.vlines[line] = (i, j)
self.ax.axhline(self.baseline, color='k', linewidth=2)
self.lineSelection = None
self.picked = None
if with_same_zoom:
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
self.canvas.toolbar.push_current()
self.canvas.draw()
def refreshTable(self):
self.table.clear()
ct = self.cycle_times
if ct is None:
return
self.table.setColumnCount(ct.shape[1])
self.table.setHeaderLabels(
['%d/%d' % (j, ct.shape[1]) for j in range(ct.shape[1])])
cmap = get_cmap('jet', self.cycle_times.shape[0])
for i in range(ct.shape[0]):
item = QTreeWidgetItem(
["%f" % ct[i, j] for j in range(ct.shape[1])])
pix = QPixmap(10, 10)
r, g, b = ColorConverter().to_rgb(cmap(i))
pix.fill(QColor(r * 255, g * 255, b * 255))
icon = QIcon(pix)
item.setIcon(0, icon)
self.table.addTopLevelItem(item)
self.table.setColumnWidth(0, 100)
def onPick(self, event):
thisline = event.artist
mouseevent = event.mouseevent
if event.artist in self.vlines:
self.picked = event.artist
def releaseEvent(self, event):
if self.picked is None: return
i, j = self.vlines[self.picked]
x = self.picked.get_xdata()
# fixme ???????
if x.size >= 2: x = x[0]
if x == numpy.array(None):
# out
self.picked.set_xdata(self.cycle_times[i, j])
self.canvas.draw()
self.picked = None
return
# test if between neightbours
ct = self.cycle_times.copy()
ct[i, j] = x
ct = ct.reshape(ct.size)
ct = ct[~numpy.isnan(ct)]
if numpy.any(numpy.diff(ct) < 0):
self.picked.set_xdata(self.cycle_times[i, j])
else:
self.cycle_times[i, j] = x
self.refreshTable()
self.canvas.draw()
self.colorSelected(i, j)
self.picked = None
def motionEvent(self, event):
if self.picked is None: return
self.picked.set_xdata(event.xdata)
i, j = self.vlines[self.picked]
if self.lineSelection is not None:
self.lineSelection.set_xdata(event.xdata)
self.canvas.draw()
def colorSelected(self, i, j):
if i is None:
if self.lineSelection is not None:
self.ax.lines.remove(self.lineSelection)
self.lineSelection = None
else:
if self.lineSelection is None:
self.lineSelection = self.ax.axvline(self.cycle_times[i, j],
color='m',
alpha=.4,
linewidth=5,
picker=False)
else:
self.lineSelection.set_xdata(self.cycle_times[i, j])
# change select in table
self.disconnect(self.table, SIGNAL('itemSelectionChanged()'),
self.newSelectionInTable)
flags = QItemSelectionModel.Select | QItemSelectionModel.Rows
itemsSelection = QItemSelection()
index = self.table.model().index(i, 0, QModelIndex())
ir = QItemSelectionRange(index)
itemsSelection.append(ir)
self.table.selectionModel().select(itemsSelection, flags)
# set selection visible
index = self.table.model().index(i, 0, QModelIndex())
item = self.table.itemFromIndex(index)
self.table.scrollToItem(item)
self.connect(self.table, SIGNAL('itemSelectionChanged()'),
self.newSelectionInTable)
self.canvas.draw()
## highlight selection
def newSelectionInTable(self):
ind = []
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
if len(ind) >= 1:
self.colorSelected(ind[0], 0)
else:
self.colorSelected(None, None)
## compute new one
def newDetection(self):
dia = QDialog()
v = QVBoxLayout()
dia.setLayout(v)
self.wMeth = WidgetMultiMethodsParam(
list_method=list_method,
method_name='<b>Choose methd for detection</b>:',
globalApplicationDict=self.globalApplicationDict,
keyformemory='methodRespiration',
)
v.addWidget(self.wMeth)
buttonBox = QDialogButtonBox(QDialogButtonBox.Ok
| QDialogButtonBox.Cancel)
v.addWidget(buttonBox)
#~ self.connect( buttonBox.buttons()[1] , SIGNAL('clicked()') , self.apply )
self.connect(buttonBox, SIGNAL('rejected()'), dia, SLOT('reject()'))
self.connect(buttonBox, SIGNAL('accepted()'), dia, SLOT('accept()'))
if dia.exec_():
method = self.wMeth.get_method()
m = method()
self.cycle_times = m.compute(self.respiration,
**self.wMeth.get_dict())
self.refreshPlot(with_same_zoom=False)
self.refreshTable()
## context menu insert and delete
def contextMenuTable(self, point):
ind = []
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
menu = QMenu()
act = menu.addAction(QIcon(':/user-trash.png'),
self.tr('Delete cycles'))
self.connect(act, SIGNAL('triggered()'), self.deleteSelectedCycles)
if len(ind) == 1:
act = menu.addAction(QIcon(':/TODO.png'),
self.tr('Insert cycle before this one'))
self.connect(act, SIGNAL('triggered()'), self.insertCycleBefore)
act = menu.addAction(QIcon(':/TODO.png'),
self.tr('Insert cycle after this one'))
self.connect(act, SIGNAL('triggered()'), self.insertCycleAfter)
menu.exec_(self.cursor().pos())
def deleteSelectedCycles(self):
ind = []
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
indOK = numpy.setdiff1d(numpy.arange(self.cycle_times.shape[0]),
numpy.array(ind))
if self.cycle_times.shape[0] - 1 in ind and numpy.isnan(
self.cycle_times[-1, -1]):
nanlast = True
else:
nanlast = False
self.cycle_times = self.cycle_times[indOK, :]
if nanlast and self.cycle_times.shape[1] > 1:
self.cycle_times[-1, 1:] = numpy.nan
self.refreshPlot(with_same_zoom=True)
self.refreshTable()
def insertCycleBefore(self):
i = self.table.selectedIndexes()[0].row()
self.insertCycle(i)
def insertCycleAfter(self):
i = self.table.selectedIndexes()[0].row() + 1
self.insertCycle(i)
def insertCycle(self, i):
n = self.cycle_times.shape[1]
ct = numpy.zeros((self.cycle_times.shape[0] + 1, n), dtype='f')
ct[:i, :] = self.cycle_times[:i, :]
ct[i + 1:, :] = self.cycle_times[i:, :]
if i != 0:
start = self.cycle_times[i - 1, -1]
else:
start = self.cycle_times[0, 0] - 1.
if i != self.cycle_times.shape[0]:
stop = self.cycle_times[i, 0]
else:
stop = self.cycle_times[-1, -1] + 1.
if numpy.isnan(stop): return
step = (stop - start) / (n + 2)
ct[i, :] = numpy.arange(start + step, stop - step, step)
self.cycle_times = ct
self.refreshPlot(with_same_zoom=True)
self.refreshTable()
def save_to_db(self):
#~ self.respiration = self.session.query(RespirationSignal).filter_by(id=self.id_respirationsignal).one()
self.respiration.cycle_times = self.cycle_times
self.session.merge(self.respiration)
self.session.commit()
self.session.expunge_all()
def reload_from_db(self):
#~ self.respiration = self.session.query(RespirationSignal).filter_by(id=self.id_respirationsignal).one()
self.cycle_times = self.respiration.cycle_times
self.refreshPlot()
self.refreshTable()
self.session.expunge_all()
class RespirationCycleEdition(QDialog) :
"""
"""
def __init__(self , parent = None ,
metadata =None,
Session = None,
session = None,
globalApplicationDict = None,
id_respirationsignal = None,
):
QDialog.__init__(self, parent)
self.metadata = metadata
self.session = Session()
self.globalApplicationDict = globalApplicationDict
self.id_respirationsignal = id_respirationsignal
self.respiration = self.session.query(RespirationSignal).filter_by(id=id_respirationsignal).one()
#FIXME: do not work:
self.setModal(False)
self.setWindowModality( Qt.NonModal )
self.setWindowTitle(self.tr('OpenElectrophy respiration for %d'%(self.respiration.id) ))
self.setWindowIcon(QIcon(':/respiration.png'))
self.mainLayout = QVBoxLayout()
self.setLayout(self.mainLayout)
h = QHBoxLayout()
self.mainLayout.addLayout( h )
c = SimpleCanvasAndTool()
h.addWidget(c, 3)
self.canvas = c.canvas
self.ax = self.canvas.fig.add_subplot(1,1,1)
v = QVBoxLayout()
h.addLayout(v , 2)
but = QPushButton(QIcon(':/TODO.txt') , 'Auto detect')
v.addWidget(but)
self.connect(but , SIGNAL('clicked()'), self.newDetection )
v.addSpacing(20)
v.addWidget(QLabel('<b>Repiratory cycles</b>') )
self.table = QTreeWidget()
#~ self.table.setMinimumWidth(100)
#~ self.table.setColumnWidth(0,80)
v.addWidget(self.table )
self.table.setSelectionMode( QAbstractItemView.ExtendedSelection)
self.connect(self.table ,SIGNAL('itemSelectionChanged()') , self.newSelectionInTable)
self.table.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self.table,SIGNAL('customContextMenuRequested( const QPoint &)'),self.contextMenuTable)
self.mainLayout.addSpacing(20)
buttonBox = QDialogButtonBox()
but = QPushButton(QIcon(':/document-save.png'),'Save to DB')
buttonBox.addButton(but , QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.save_to_db)
but = QPushButton(QIcon(':/reload.png'),'Reload from DB')
buttonBox.addButton(but , QDialogButtonBox.ActionRole)
self.connect(but, SIGNAL('clicked()'), self.reload_from_db)
but = QPushButton(QIcon(':/window-close.png') , 'Quit')
buttonBox.addButton(but , QDialogButtonBox.RejectRole)
self.connect(but, SIGNAL('clicked()'), self.close)
self.mainLayout.addWidget(buttonBox)
if self.respiration.cycle_times is None:
self.cycle_times = None
else:
self.cycle_times = self.respiration.cycle_times
self.vlines = { }
self.baseline = 0.
self.refreshPlot()
self.refreshTable()
self.canvas.mpl_connect('pick_event', self.onPick)
self.canvas.mpl_connect('button_release_event', self.releaseEvent)
self.canvas.mpl_connect('motion_notify_event', self.motionEvent)
#~ self.picked = None
#~ self.lineSelection = None
self.session.expunge_all()
def refreshPlot(self, with_same_zoom = False):
if with_same_zoom:
if self.canvas.toolbar._views.empty(): self.canvas.toolbar.push_current()
#~ self.canvas.toolbar.push_current()
xlim = self.ax.get_xlim()
ylim = self.ax.get_ylim()
self.ax.clear()
t = self.respiration.t()
sig = self.respiration.signal
self.ax.plot(t,sig, 'b')
if self.cycle_times is not None:
self.vlines = { }
cmap = get_cmap('jet' , self.cycle_times.shape[0])
for i in range(self.cycle_times.shape[0]):
for j in range(self.cycle_times.shape[1]):
if j==0: ls = '-'
else: ls = '--'
line = self.ax.axvline( self.cycle_times[i,j] , color = cmap(i) , linestyle = ls , picker = 3 , linewidth = 1.5)
self.vlines[line] = (i,j)
self.ax.axhline( self.baseline, color = 'k', linewidth = 2)
self.lineSelection = None
self.picked = None
if with_same_zoom:
self.ax.set_xlim(xlim)
self.ax.set_ylim(ylim)
self.canvas.toolbar.push_current()
self.canvas.draw()
def refreshTable(self):
self.table.clear()
ct = self.cycle_times
if ct is None:
return
self.table.setColumnCount( ct.shape[1])
self.table.setHeaderLabels( [ '%d/%d'%(j,ct.shape[1]) for j in range( ct.shape[1]) ])
cmap = get_cmap('jet' , self.cycle_times.shape[0])
for i in range(ct.shape[0]):
item = QTreeWidgetItem(["%f"%ct[i,j] for j in range( ct.shape[1]) ])
pix = QPixmap(10,10 )
r,g,b = ColorConverter().to_rgb(cmap(i) )
pix.fill(QColor(r*255,g*255,b*255 ))
icon = QIcon(pix)
item.setIcon(0,icon)
self.table.addTopLevelItem(item)
self.table.setColumnWidth(0,100)
def onPick(self, event):
thisline = event.artist
mouseevent = event.mouseevent
if event.artist in self.vlines:
self.picked = event.artist
def releaseEvent(self, event):
if self.picked is None: return
i,j = self.vlines[self.picked]
x = self.picked.get_xdata()
# fixme ???????
if x.size>=2: x = x[0]
if x == numpy.array(None):
# out
self.picked.set_xdata(self.cycle_times[i,j])
self.canvas.draw()
self.picked = None
return
# test if between neightbours
ct = self.cycle_times.copy()
ct[i,j] = x
ct = ct.reshape(ct.size)
ct = ct[~numpy.isnan(ct)]
if numpy.any(numpy.diff(ct)<0):
self.picked.set_xdata(self.cycle_times[i,j])
else:
self.cycle_times[i,j] = x
self.refreshTable()
self.canvas.draw()
self.colorSelected(i,j)
self.picked = None
def motionEvent(self, event):
if self.picked is None: return
self.picked.set_xdata(event.xdata)
i,j = self.vlines[self.picked]
if self.lineSelection is not None:
self.lineSelection.set_xdata(event.xdata)
self.canvas.draw()
def colorSelected(self, i , j):
if i is None:
if self.lineSelection is not None:
self.ax.lines.remove(self.lineSelection)
self.lineSelection = None
else:
if self.lineSelection is None:
self.lineSelection = self.ax.axvline( self.cycle_times[i,j] , color ='m' , alpha = .4, linewidth = 5 , picker = False)
else:
self.lineSelection.set_xdata(self.cycle_times[i,j])
# change select in table
self.disconnect(self.table ,SIGNAL('itemSelectionChanged()') , self.newSelectionInTable)
flags = QItemSelectionModel.Select | QItemSelectionModel.Rows
itemsSelection = QItemSelection()
index = self.table.model().index(i,0,QModelIndex())
ir = QItemSelectionRange( index )
itemsSelection.append( ir )
self.table.selectionModel().select( itemsSelection , flags)
# set selection visible
index = self.table.model().index(i,0,QModelIndex())
item = self.table.itemFromIndex(index)
self.table.scrollToItem( item )
self.connect(self.table ,SIGNAL('itemSelectionChanged()') , self.newSelectionInTable)
self.canvas.draw()
## highlight selection
def newSelectionInTable(self):
ind = [ ]
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
if len(ind)>=1 :
self.colorSelected(ind[0] , 0)
else:
self.colorSelected(None,None)
## compute new one
def newDetection(self):
dia = QDialog()
v = QVBoxLayout()
dia.setLayout(v)
self.wMeth = WidgetMultiMethodsParam( list_method = list_method,
method_name = '<b>Choose methd for detection</b>:',
globalApplicationDict = self.globalApplicationDict,
keyformemory = 'methodRespiration',
)
v.addWidget( self.wMeth )
buttonBox = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel)
v.addWidget(buttonBox)
#~ self.connect( buttonBox.buttons()[1] , SIGNAL('clicked()') , self.apply )
self.connect( buttonBox , SIGNAL('rejected()') , dia, SLOT('reject()') )
self.connect( buttonBox , SIGNAL('accepted()') , dia, SLOT('accept()') )
if dia.exec_():
method = self.wMeth.get_method()
m = method()
self.cycle_times =m.compute(self.respiration, **self.wMeth.get_dict() )
self.refreshPlot( with_same_zoom = False )
self.refreshTable( )
## context menu insert and delete
def contextMenuTable(self, point):
ind = [ ]
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
menu = QMenu()
act = menu.addAction(QIcon(':/user-trash.png'), self.tr('Delete cycles'))
self.connect(act,SIGNAL('triggered()') ,self.deleteSelectedCycles)
if len(ind)==1:
act = menu.addAction(QIcon(':/TODO.png'), self.tr('Insert cycle before this one'))
self.connect(act,SIGNAL('triggered()') ,self.insertCycleBefore)
act = menu.addAction(QIcon(':/TODO.png'), self.tr('Insert cycle after this one'))
self.connect(act,SIGNAL('triggered()') ,self.insertCycleAfter)
menu.exec_(self.cursor().pos())
def deleteSelectedCycles(self):
ind = [ ]
for index in self.table.selectedIndexes():
if index.column() == 0: ind.append(index.row())
indOK = numpy.setdiff1d(numpy.arange(self.cycle_times.shape[0]) , numpy.array(ind))
if self.cycle_times.shape[0]-1 in ind and numpy.isnan(self.cycle_times[-1,-1]):
nanlast = True
else:
nanlast = False
self.cycle_times = self.cycle_times[indOK,:]
if nanlast and self.cycle_times.shape[1] >1:
self.cycle_times[-1,1:] = numpy.nan
self.refreshPlot( with_same_zoom = True )
self.refreshTable( )
def insertCycleBefore(self):
i = self.table.selectedIndexes()[0].row()
self.insertCycle(i)
def insertCycleAfter(self):
i = self.table.selectedIndexes()[0].row() + 1
self.insertCycle(i)
def insertCycle(self, i):
n = self.cycle_times.shape[1]
ct = numpy.zeros( (self.cycle_times.shape[0]+1, n) , dtype = 'f')
ct[:i , :] = self.cycle_times[:i,:]
ct[i+1: , :] = self.cycle_times[i:,:]
if i!=0:
start = self.cycle_times[i-1,-1]
else:
start = self.cycle_times[0,0]-1.
if i!=self.cycle_times.shape[0]:
stop = self.cycle_times[i,0]
else:
stop = self.cycle_times[-1,-1]+1.
if numpy.isnan(stop): return
step = (stop-start)/(n+2)
ct[i,:] = numpy.arange(start+step, stop-step, step)
self.cycle_times = ct
self.refreshPlot( with_same_zoom = True )
self.refreshTable( )
def save_to_db(self):
#~ self.respiration = self.session.query(RespirationSignal).filter_by(id=self.id_respirationsignal).one()
self.respiration.cycle_times = self.cycle_times
self.session.merge(self.respiration)
self.session.commit()
self.session.expunge_all()
def reload_from_db(self):
#~ self.respiration = self.session.query(RespirationSignal).filter_by(id=self.id_respirationsignal).one()
self.cycle_times = self.respiration.cycle_times
self.refreshPlot( )
self.refreshTable( )
self.session.expunge_all()
def saveAsFile(parent=None,
ids =None,
tablenames = None,
metadata = None,
Session = None,
session = None,
globalApplicationDict = None, ):
# mode homogeneous
tablename = tablenames[0]
session = Session()
OEclass = metadata.dictMappedClasses[tablename]
from ..io.io import all_format
list_formats = [ ]
formats ={ }
for name, d in all_format:
wo = [ o.__name__.lower() for o in d['class'].writeable_objects ]
if tablename in wo:
class F:
pass
f = F()
f.name = name
f.params = d['class'].write_params[ OEclass ]
list_formats.append( f )
formats[name] = d['class']
dia = QDialog()
dia.setWindowFlags(Qt.Dialog)
v = QVBoxLayout()
dia.setLayout(v)
mwp = WidgetMultiMethodsParam( parent = parent ,
list_method = list_formats,
method_name = 'Export selected '+tablename,
globalApplicationDict = globalApplicationDict,
)
v.addWidget( mwp )
params = [
[ 'dir' , { 'value' : '' , 'widgettype' : ChooseDirWidget , 'label' : 'Select path to write files' }],
]
place = ParamWidget(
params,
applicationdict = globalApplicationDict,
title = None,
)
v.addWidget( place )
buttonBox = QDialogButtonBox(QDialogButtonBox.Ok)
v.addWidget(buttonBox)
dia.connect(buttonBox, SIGNAL('accepted()'), dia, SLOT('accept()'));
if dia.exec_():
name = mwp.get_name()
options = mwp.get_dict()
dir = place['dir']
for id in ids:
OEinstance = session.query(OEclass).filter_by(id=id).one()
IOinstance = formats[name](filename = os.path.join( dir, OEinstance.name+'.'+formats[name].extensions[0] ) )
if OEclass ==Segment:
IOinstance.write_segment( OEinstance, **options)
elif OEclass ==Block:
IOinstance.write_block( OEinstance, **options)