def view(self, target):
"""
view with viewer
"""
# prepare viewer
if not self.aui:
self.aui = aui.MyFrame(parent=self)
self.aui.Show()
if isinstance(target,
six.string_types) and chromformat.is_chromagnon(target):
newpanel = chromeditor.ChromagnonEditor(self.aui, target)
else:
newpanel = aui.ImagePanel(self.aui, target)
if isinstance(target, six.string_types):
name = os.path.basename(target)
else:
name = target.file
if sys.platform in ('linux2', 'win32'):
wx.CallAfter(self.aui.imEditWindows.addPage,
newpanel,
name,
select=True)
else:
self.aui.imEditWindows.addPage(newpanel, name, select=True)
def OnChooseInitGuess(self, evt=None):
"""
set reference files
"""
wildcard = '*.chromagnon*'
if os.name == 'posix':
dlg = G.FileSelectorDialog(self,
direc=self.lastpath,
wildcard=wildcard,
multiple=False)
else:
dlg = wx.FileDialog(self,
'Choose chromagnon files',
defaultDir=self.lastpath,
wildcard=wildcard)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
if chromformat.is_chromagnon(fn, True):
self._setInitGuess(fn)
else:
G.openMsg(parent=self,
msg='The file is not a valid chromagnon file',
title="Warning")
def _load_func(self, fn):
if chromformat.is_chromagnon(fn):
h = chromformat.ChromagnonReader(fn)
else:
try:
h = imgio.Reader(fn)
except ValueError as e:
return listbox.imgio_dialog(e, self)
if aligner.hasSameWave(h):
dlg = wx.MessageDialog(
self,
'The image contains multiple channels with the same wavelength. Please use a unique wavelength for each channel',
'Error in channel wavelengths',
wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
if h.nseries > 1:
dlg = wx.MessageDialog(
self,
'Multiple series data sets are not allowed, please make a file with a single image in a file',
'Error in image file', wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
self.lastpath = os.path.dirname(fn)
C.saveConfig(lastpath=self.lastpath)
return h
def view(self, target):
"""
view with viewer
"""
# prepare viewer
if not self.aui:
if self.parent and not self.parent.aui:
self.aui = aui.MyFrame(parent=self.parent)
self.parent.aui = self.aui
self.aui.Show()
elif not self.parent:
self.aui = aui.MyFrame(parent=self)
self.aui.Show()
elif self.parent and self.parent.aui:
self.aui = self.parent.aui
# draw
if isinstance(target, six.string_types):
if chromformat.is_chromagnon(target):
target_is_image = False
else:
target_is_image = True
an = aligner.Chromagnon(target)
else:
an = target
target_is_image = True
if target_is_image:
newpanel = aui.ImagePanel(self.aui, an.img)
else:
#an.close()
newpanel = chromeditor.ChromagnonEditor(self.aui, target)
if isinstance(target, six.string_types):
name = os.path.basename(target)
else:
name = target.file
if sys.platform in ('linux2', 'win32'):
wx.CallAfter(self.aui.imEditWindows.addPage,
newpanel,
name,
select=True)
else:
self.aui.imEditWindows.addPage(newpanel, name, select=True)
def _load_func(self, fn):
if chromformat.is_chromagnon(fn):
h = chromformat.ChromagnonReader(fn)
else:
try:
h = bioformatsIO.load(fn)
except ValueError:
dlg = wx.MessageDialog(self,
'%s is not a valid image file!' % ff,
'Error reading image file',
wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
if h.nseries > 1:
dlg = wx.MessageDialog(
self,
'Multiple series data sets are not allowed, please make a file with a single image in a file',
'Error in image file', wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
return h
def run(self):
"""
This function execute the series of processes
Since it uses GUI, this function uses several events to control GUI
They are called by wx.PostEvent()
"""
OLD_SCIK = fftmanager.SCIK
OLD_REIK = fftmanager.REIK
fftmanager.SCIK = False
fftmanager.REIK = False
fns = self.fns
targets = self.targets
parms = self.parms
# parameters
cutout = parms[0]
initGuess = parms[1]
if initGuess and not os.path.isfile(initGuess):
raise ValueError(
'The initial guess is not a valid Chromagnon file')
local = parms[2]
maxShift = parms[3]
zmag = parms[4]
self.parm_suffix = parms[5]
self.img_suffix = parms[6]
nts = parms[7]
self.img_ext = parms[8]
min_pxls_yx = parms[9]
saveAlignParam = True
alignChannels = True
alignTimeFrames = True
outs0 = []
outs = []
doneref = []
donetgt = []
errs = []
kwds = {}
self.progress(0)
try:
# calibration
for index, fn in enumerate(fns):
#clk0 = time.clock()
# calculation
if not chromformat.is_chromagnon(fn):
tstf = time.strftime('%Y %b %d %H:%M:%S', time.localtime())
self.log('\n**Measuring shifts in %s at %s' %
(os.path.basename(fn), tstf))
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['ref', index, wx.RED]))
an = aligner.Chromagnon(fn)
an = self.getAligner(fn, index, what='ref')
an.setZmagSwitch(zmag)
an.setMaxShift(maxShift)
pgen = self.progressValues(target=False,
an=an,
alignChannels=alignChannels,
alignTimeFrames=alignTimeFrames,
local=local)
an.setProgressfunc(pgen)
if initGuess:
an.loadParm(initGuess)
# mapyx should not be inherited...
an.mapyx = None
if (an.nw > 1 and an.nt == 1):
an.findBestChannel()
self.echo('Calculating channel alignment...')
for t in range(an.nt):
try:
an.findAlignParamWave(t=t)
except alignfuncs.AlignError: # in xcorr or else
self.echo('Calculation failed, skipping')
errs.append(index)
continue
if local in self.localChoice[1:]:
an.findNonLinear2D(t=t, npxls=min_pxls_yx)
if local in self.localChoice[2:]:
arr = an.findNonLinear3D(t=t,
npxls=min_pxls_yx)
del arr
elif an.nt > 1:
self.echo('Calculating timelapse alignment...')
an.findBestChannel()
an.findBestTimeFrame(an.refwave)
an.findAlignParamTime(doWave=False)
fn = an.saveParm()
currlist = None
#clk1 = time.clock()
#print('Done seconds', (clk1-clk0))
an.close()
doneref.append(index)
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['ref', index, wx.BLUE]))
if index < len(targets):
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['tgt', index, wx.RED]))
target = targets[index]
tstf = time.strftime('%Y %b %d %H:%M:%S', time.gmtime())
self.log(
'\n**Applying to %s using %s at %s' %
(os.path.basename(target), os.path.basename(fn), tstf))
an = self.getAligner(target, index, what='target')
pgen = self.progressValues(target=True, an=an)
an.setProgressfunc(pgen)
self.progress(0)
an.loadParm(fn)
#if cutout:
an.setRegionCutOut(cutout)
out = an.saveAlignedImage()
donetgt.append(index)
an.close()
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['tgt', index, wx.BLUE]))
if self.notify_obj:
wx.PostEvent(self.notify_obj,
MyEvent(EVT_VIEW_ID, [out]))
elif self.notify_obj:
wx.PostEvent(self.notify_obj, MyEvent(EVT_VIEW_ID, [fn]))
# remaining target files use the last alignment file
for index, target in enumerate(targets[len(fns):]):
index += len(fns)
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['tgt', index, wx.BLUE]))
target = targets[index]
tstf = time.strftime('%Y %b %d %H:%M:%S', time.gmtime())
if fns:
self.log(
'\n**Applying to %s using %s at %s' %
(os.path.basename(target), os.path.basename(fn), tstf))
else:
self.log('\n**Applying to %s at %s' %
(os.path.basename(target), tstf))
an = self.getAligner(target, index, what='target')
pgen = self.progressValues(target=True, an=an)
an.setProgressfunc(pgen)
self.progress(0)
if len(fns):
an.loadParm(fn)
an.setRegionCutOut(cutout)
out = an.saveAlignedImage()
donetgt.append(index)
an.close()
if self.notify_obj:
wx.PostEvent(
self.notify_obj,
MyEvent(EVT_COLOR_ID, ['tgt', index, wx.BLUE]))
#wx.PostEvent(self.notify_obj, MyEvent(EVT_PROGRESS_ID, [prange.pop(0)]))
# pgen.next()
#out = aligner.Chromagnon(out)
if self.notify_obj:
print('event view', out)
wx.PostEvent(self.notify_obj, MyEvent(EVT_VIEW_ID, [out]))
except MyError:
if self.notify_obj:
wx.PostEvent(self.notify_obj, MyEvent(EVT_ABORT_ID, []))
wx.PostEvent(self.notify_obj, MyEvent(EVT_PROGRESS_ID, [0]))
else:
pass
except:
#exc_type, exc_value, exc_traceback = sys.exc_info()
#formatted = traceback.format_exception(exc_type, exc_value, exc_traceback)
if self.notify_obj:
import traceback, sys
wx.PostEvent(self.notify_obj,
MyEvent(EVT_ERROR_ID,
sys.exc_info())) #formatted]))
#wx.PostEvent(self.notify_obj, MyEvent(EVT_PROGRESS_ID, [0]))
self.progress(0)
else:
pass
else:
if self.notify_obj:
wx.PostEvent(self.notify_obj,
MyEvent(EVT_DONE_ID, [doneref, donetgt, errs]))
#wx.PostEvent(self.notify_obj, MyEvent(EVT_PROGRESS_ID, [0]))
self.progress(0)
else:
pass
finally:
self.logh.close()
#bioformatsIO.uninit_javabridge()
fftmanager.SCIK = OLD_SCIK
fftmanager.REIK = OLD_REIK