def load_clicked(self):
"""
Checks that directory is pointed at a slice
Check LIMS for 20x biocytin image and if 20x image is saved locally.
If image not saved locally then copies file from LIMS.
Enables button to create a JSON of the cell locations
"""
if self.base_dir.info()['dirType'] != 'Slice':
raise Exception('No Slice Selected')
self.base_path = self.base_dir.name()
aff_image_path = lims.specimen_20x_image(self.specimen_name,
treatment='Biocytin')
if aff_image_path is None:
raise Exception("No 20x biocytin image for specimen %s" %
self.specimen_name)
if not os.path.exists(aff_image_path):
raise Exception("No image found at path '%s'" % aff_image_path)
aff_image_name = os.path.split(aff_image_path)[-1]
save_path = os.path.join(self.base_path, aff_image_name)
if not os.path.exists(save_path):
with pg.BusyCursor():
shutil.copy2(aff_image_path, save_path)
self.base_dir.indexFile(aff_image_name)
def storeDBScan(self, scan, storeEvents=True):
"""Store all data for a scan, using cached values if possible"""
p = debug.Profiler("Photostim.storeDBScan", disabled=True)
if storeEvents:
self.clearDBScan(scan)
with pg.BusyCursor():
#dh = scan.source()
#print "Store scan:", scan.source().name()
events = []
stats = []
spots = scan.spots()
with pg.ProgressDialog("Preparing data for %s" % scan.name(), 0,
len(spots) + 1) as dlg:
## collect events and stats from all spots in the scan
for i in xrange(len(spots)):
s = spots[i]
fh = self.dataModel.getClampFile(s.data())
try:
ev = scan.getEvents(fh)['events']
events.append(ev)
except:
print fh, scan.getEvents(fh)
raise
st = scan.getStats(s.data())
stats.append(st)
dlg.setValue(i)
if dlg.wasCanceled():
raise HelpfulException("Scan store canceled by user.",
msgType='status')
p.mark("Prepared data")
dbui = self.getElement('Database')
db = dbui.getDb()
with db.transaction():
## Store all events for this scan
if storeEvents:
events = [x for x in events if len(x) > 0]
if len(events) > 0:
ev = np.concatenate(events)
p.mark("concatenate events")
self.detector.storeToDB(ev)
p.mark("stored all events")
## Store spot data
self.storeStats(stats)
p.mark("stored all stats")
p.finish()
def __init__(self, **kwds):
if not HAVE_AICCF:
raise Exception(
"This item requires the aiccf module, but it could not be imported."
)
kwds.pop('viewRect', None)
self.atlas = CCFAtlasData()
with pg.BusyCursor():
self.atlasView = AtlasSliceView()
self.atlasView.set_data(self.atlas)
item = self.atlasView.img2
opts = {'scalable': True, 'rotatable': True, 'movable': True}
opts.update(kwds)
CanvasItem.__init__(self, item, **opts)
self.__ctrl = Qt.QWidget()
self.__layout = Qt.QGridLayout()
self.__ctrl.setLayout(self.__layout)
self.__layout.setContentsMargins(0, 0, 0, 0)
self.__layout.addWidget(self.atlasView.display_ctrl, 0, 0)
self.__layout.addWidget(self.atlasView.label_tree, 1, 0)
self.showSliceBtn = Qt.QPushButton("Show slice")
self.showSliceBtn.setCheckable(True)
self.__layout.addWidget(self.showSliceBtn, 2, 0)
self.showSliceBtn.toggled.connect(self.showSliceToggled)
self.layout.addWidget(self.__ctrl, self.layout.rowCount(), 0, 1, 2)
# Set up window for selecting slice plane
self.sliceWidget = Qt.QWidget()
self.sliceLayout = Qt.QGridLayout()
self.sliceWidget.setLayout(self.sliceLayout)
self.sliceGraphicsView = pg.GraphicsLayoutWidget()
self.sliceLayout.addWidget(self.sliceGraphicsView, 0, 0)
self.sliceView = self.sliceGraphicsView.addViewBox()
self.sliceView.addItem(self.atlasView.img1)
self.sliceView.autoRange()
self.sliceView.setAspectLocked(True)
self.sliceView.addItem(self.atlasView.line_roi)
self.sliceLayout.addWidget(self.atlasView.zslider, 1, 0)
self.sliceLayout.addWidget(self.atlasView.angle_slider, 2, 0)
self.sliceWidget.resize(800, 800)
def setCurrentFile(self, file):
#print "=============== set current file ============"
if file is self.current:
return
## What if we just want to update the data display?
#self.clear()
if file is None:
self.current = None
return
if file.isDir():
## Sequence or not?
return
else:
typ = file.fileType()
if typ is None:
return
else:
image = False
with pg.BusyCursor():
data = file.read()
if typ == 'ImageFile':
image = True
elif typ == 'MetaArray':
if data.ndim == 2 and not data.axisHasColumns(
0) and not data.axisHasColumns(1):
image = True
elif data.ndim > 2:
image = True
else:
return
with pg.BusyCursor():
if image:
if self.currentType == 'image' and len(self.widgets) > 0:
try:
self.widgets[0].setImage(data, autoRange=False)
except:
print "widget types:", map(type, self.widgets)
raise
else:
self.clear()
w = pg.ImageView(self)
#print "add image:", w.ui.roiPlot.plotItem
#self.plots = [weakref.ref(w.ui.roiPlot.plotItem)]
self.addWidget(w)
w.setImage(data)
self.widgets.append(w)
self.currentType = 'image'
else:
self.clear()
w = pg.MultiPlotWidget(self)
self.addWidget(w)
w.plot(data)
self.currentType = 'plot'
self.widgets.append(w)
#print "add mplot:", w.mPlotItem.plots
#self.plots = [weakref.ref(p[0]) for p in w.mPlotItem.plots]
if (hasattr(data, 'implements') and data.implements('MetaArray')):
if self.dictWidget is None:
w = DictView(data._info)
self.dictWidget = w
#w.setText(str(data._info[-1]))
self.addWidget(w)
self.widgets.append(w)
h = self.size().height()
self.setSizes([h * 0.8, h * 0.2])
else:
self.dictWidget.setData(data._info)
def load_data(self, seqDir):
with pg.BusyCursor():
self._load_data(seqDir)
