def OnChooseTargetFiles(self, evt):
"""
set reference files
"""
confdic = C.readConfig()
wildcard = confdic.get('lastwildcard', FILTER)
ll = self.listTgt
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, self.lastpath, wildcard=wildcard)
else:
dlg = wx.FileDialog(self, 'Choose %s files' % listtype, defaultDir=self.lastpath, style=wx.FD_MULTIPLE)
if dlg.ShowModal() == wx.ID_OK:
fns = dlg.GetPaths()
if not fns:
return
if os.name == 'posix':
wildcard = dlg.fnPat
if isinstance(fns, basestring):
fns = [fns]
ll.addFiles(fns)
self.lastpath = os.path.dirname(fns[0])
C.saveConfig(lastwildcard=wildcard, lastpath=self.lastpath)
self.checkGo()
def OnGo(self, ev=None):
"""
run or cancel the alignment program
The actual sequence of processes is written in threads.ThreadWithExc.run()
"""
if self.goButton.GetValue():
if not self.listRef.columnkeys:
return
fns = [os.path.join(*self.listRef.getFile(index)[:2]) for index in self.listRef.columnkeys]
targets = [os.path.join(*self.listTgt.getFile(index)[:2]) for index in self.listTgt.columnkeys]
# run program
parms = [self.flat_suffix_txt.GetValue(),
self.flatimg_suffix_txt.GetValue(),
self.outextch.GetStringSelection()]
gui = threads.GUImanager(self, __name__)
self.th = threads.ThreadFlat(gui, None, fns, targets, parms)#, extrainfo)
self.th.start()
C.saveConfig(flat_suffix_txt=parms[0], flatimg_suffix_txt=parms[1], flatfn=fns[0], flat_format=parms[2])
else:
tid = self.th._get_my_tid()
#stopit.async_raise(tid, threads.MyError)
threads.async_raise(tid, threads.MyError)
def OnChooseReferenceFile(self, evt):
"""
set reference files
"""
confdic = C.readConfig()
wildcard = confdic.get('lastwildcard', FILTER)
ll = self.listRef
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, direc=self.lastpath, wildcard=wildcard, multiple=False)
else:
dlg = wx.FileDialog(self, 'Choose %sfiles' % listtype, defaultDir=self.lastpath, wildcard=wildcard)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
if not fn:
return
if os.name == 'posix':
wildcard = dlg.fnPat
ll.clearAll()
ll.addFiles([fn])
self.lastpath = os.path.dirname(fn)
C.saveConfig(lastwildcard=wildcard, lastpath=self.lastpath)
self.checkGo()
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 _setFlat(self, fns):
#ids = range(len(fns))
#ids.reverse()
#[self.listRef.clearRaw(i) for i in ids]
self.listRef.clearAll()
for i, fn in enumerate(fns):
self.listRef.addFile(fn)
C.saveConfig(flatfn=fns[0])
def OnChooseImgFiles(self, evt, listtype='ref'):
"""
set reference files
"""
confdic = C.readConfig()
if listtype == 'ref':
ll = self.listRef
wildcard = confdic.get('lastwildcardref', FILTER)
else:
ll = self.listTgt
wildcard = confdic.get('lastwildcardtgt', FILTER)
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, self.lastpath, wildcard=wildcard)
else:
dlg = wx.FileDialog(self,
'Choose %s files' % listtype,
defaultDir=self.lastpath,
style=wx.FD_MULTIPLE)
if dlg.ShowModal() == wx.ID_OK:
fns = dlg.GetPaths()
if not fns:
return
if os.name == 'posix':
wildcard = dlg.fnPat
if isinstance(fns, six.string_types): #str):
fns = [fns]
ll.addFiles(fns)
if listtype != 'ref':
if any([nw > 5 for nw in ll.nws
]) and self.outextch.GetStringSelection() == (
os.path.extsep + aligner.WRITABLE_FORMATS[1]):
self.outextch.SetStringSelection(
os.path.extsep + aligner.WRITABLE_FORMATS[0])
G.openMsg(
parent=self,
msg=
'Since number of wavelength in some image file is more than 5,\nthe output file format was changed to tiff',
title="Output file format change")
self.lastpath = os.path.dirname(fns[0])
if listtype == 'ref':
C.saveConfig(lastwildcardref=wildcard, lastpath=self.lastpath)
else:
C.saveConfig(lastwildcardtgt=wildcard, lastpath=self.lastpath)
self.checkGo()
def onChooseFile(self, evnt):
"""
get image file
call self.view()
"""
confdic = C.readConfig()
lastpath = confdic.get('lastpath', '')
#parent = self.GetTopLevelParent()
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, lastpath)
else:
dlg = wx.FileDialog(self, 'Choose a file', defaultDir=lastpath)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
else:
return
self.view(fn)
C.saveConfig(lastpath=os.path.dirname(fn))
def onChooseFile(self, evnt):
"""
get image file
call self.view()
"""
confdic = C.readConfig()
lastpath = confdic.get('lastpath', '')
#parent = self.GetTopLevelParent()
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, lastpath)
else:
dlg = wx.FileDialog(self, 'Choose a file', defaultDir=lastpath)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
else:
return
self.view(fn)
C.saveConfig(lastpath=os.path.dirname(fn))
def onChooseOriginalFile(self, ev):
"""
get image file
"""
confdic = C.readConfig()
lastpath = confdic.get('lastpath', '')
wildcard = confdic.get('localfnpat', '*')
#parent = self.GetTopLevelParent()
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, lastpath, wildcard)
else:
dlg = wx.FileDialog(self, 'Choose a file', defaultDir=lastpath)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
else:
return
self.originalFileTxt.SetValue(fn)
C.saveConfig(lastpath=os.path.dirname(fn), localfnpat=dlg.fnPat)
def onChooseOriginalFile(self, ev):
"""
get image file
"""
confdic = C.readConfig()
lastpath = confdic.get('lastpath', '')
wildcard = confdic.get('localfnpat', '*')
#parent = self.GetTopLevelParent()
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, lastpath, wildcard)
else:
dlg = wx.FileDialog(self, 'Choose a file', defaultDir=lastpath)
if dlg.ShowModal() == wx.ID_OK:
fn = dlg.GetPath()
else:
return
self.originalFileTxt.SetValue(fn)
C.saveConfig(lastpath=os.path.dirname(fn), localfnpat=dlg.fnPat)
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 OnExtraParamButton(self, evt=None):
confdic = C.readConfig()
dlg = extrapanel.ExtraDialog(self, self.listRef, confdic, outdir=self.extra_parms.get('outdir'), refwave=str(self.extra_parms.get('refwave')))
val = dlg.ShowModal()
self.outdir = self.refwave = self.zacuur = None
if val == wx.ID_OK:
if not (dlg.outdir_cb.GetValue()):
self.extra_parms['outdir'] = dlg.outdir
C.saveConfig(outdir=dlg.outdir)
if hasattr(dlg, 'refwave_cb') and not (dlg.refwave_cb.GetValue()):
refwave = dlg.refwave_choice.GetStringSelection()
try:
refwave = eval(refwave)
except (TypeError, ValueError):
pass
self.extra_parms['refwave'] = refwave
if hasattr(dlg, 'tseriesListChoice'):
self.extra_parms['tseries4wave'] = dlg.tseriesListChoice.GetStringSelection()
self.extra_parms['zacuur'] = eval(dlg.accurListChoice.GetStringSelection())
C.saveConfig(accur=self.extra_parms['zacuur'])
self.extra_parms['max_shift'] = eval(dlg.maxshift_text.GetValue())
C.saveConfig(max_shift=self.extra_parms['max_shift'])
dlg.Destroy()
def OnChooseImgFiles(self, evt, listtype='ref'):
"""
set reference files
"""
confdic = C.readConfig()
if listtype == 'ref':
ll = self.listRef
wildcard = confdic.get('lastwildcardref', FILTER)
else:
ll = self.listTgt
wildcard = confdic.get('lastwildcardtgt', FILTER)
if os.name == 'posix':
dlg = G.FileSelectorDialog(self, self.lastpath, wildcard=wildcard)
else:
dlg = wx.FileDialog(self, 'Choose %s files' % listtype, defaultDir=self.lastpath, style=wx.FD_MULTIPLE)
if dlg.ShowModal() == wx.ID_OK:
fns = dlg.GetPaths()
if not fns:
return
if os.name == 'posix':
wildcard = dlg.fnPat
if isinstance(fns, six.string_types):
fns = [fns]
ll.addFiles(fns)
if listtype != 'ref':
if any([nw > 5 for nw in ll.nws]) and self.outextch.GetStringSelection() == (os.path.extsep + aligner.WRITABLE_FORMATS[1]):
self.outextch.SetStringSelection(os.path.extsep + aligner.WRITABLE_FORMATS[0])
G.openMsg(parent=self, msg='Since number of wavelength in some image file is more than 5,\nthe output file format was changed to tiff', title="Output file format change")
self.lastpath = os.path.dirname(fns[0])
if listtype == 'ref':
C.saveConfig(lastwildcardref=wildcard, lastpath=self.lastpath)
else:
C.saveConfig(lastwildcardtgt=wildcard, lastpath=self.lastpath)
self.checkGo()
def OnGo(self, ev=None):
"""
run or cancel the alignment program
The actual sequence of processes is written in threads.ThreadWithExc.run()
"""
if self.goButton.GetValue():
if not self.listRef.columnkeys:
return
fns = [os.path.join(*self.listRef.getFile(index)[:2]) for index in self.listRef.columnkeys]
targets = [os.path.join(*self.listTgt.getFile(index)[:2]) for index in self.listTgt.columnkeys]
# other parameters
#initguess = ''
confdic = C.readConfig()
form = self.outextch.GetStringSelection()
if not form:
self.quit('Please select the output file format next to the Suffix text box', title="The format type is missing")
return
# check wavelengths
waves1 = [list(map(int, self.listRef.getFile(index)[2].split(','))) for index in self.listRef.columnkeys]
waves2 = [list(map(int, self.listTgt.getFile(index)[2].split(','))) for index in self.listTgt.columnkeys]
nts = all([t == 1 for t in self.listRef.nts])
ids = af.checkWaves(waves1, waves2)
if ids is not None and nts:
for i, listbox in zip(ids, (self.listRef, self.listTgt)):
listbox.SetItemTextColour(i, 'purple')
#listbox.SetBackGroundColour(i, 'gray')
msg = 'Less than two Common wavelengths were found at least in %s and %s\n\nThe program will not run.' % (self.listRef.getFile(ids[0])[1], self.listTgt.getFile(ids[1])[1])
self.quit(msg, title='Error in input files')
return
# averaging
if self.averageCb.GetValue() and len(fns) > 1:
if any([waves1[0] != ws1 for ws1 in waves1[1:]]):
self.quit('There are inconsistency in channel composition in the reference files', title="Reference files are not appropriate for averaging")
return
try:
self.label.SetLabel('averaging...')
self.label.SetForegroundColour('red')
wx.Yield()
ave_fn = af.averageImage(fns, ext=form)
except Exception as e:
self.quit(e.args[0], title="Reference files are not appropriate for averaging")
return
self.listRef.clearAll()
self.listRef.addFile(ave_fn)
fns = [ave_fn]
elif self.averageCb.GetValue() and len(fns) == 1:
self.averageCb.SetValue(0)
accur = self.extra_parms.get('zacuur', confdic.get('accur', aligner.ACCUR_CHOICE[0]))
if accur in aligner.ACCUR_CHOICE_DIC:
accur = aligner.ACCUR_CHOICE_DIC[accur]
# parameters
parms = [self.cutoutCb.GetValue(),
self.extra_parms.get('outdir'),#initguess,
self.localListChoice.GetStringSelection(),
self.extra_parms.get('refwave'), #None, #self.maxShift.GetValue(),
int(accur),#self.extra_parms.get('zacuur', confdic.get('accur', aligner.ACCUR_CHOICE[0]))), #self.accurListChoice.GetStringSelection(),
self.parm_suffix_txt.GetValue(),
self.img_suffix_txt.GetValue(),
self.extra_parms.get('tseries4wave', 'time'),#[nt for nt in self.listRef.nts], # copy
form,
int(self.min_pxls_choice.GetStringSelection()),
self.extra_parms.get('max_shift', af.MAX_SHIFT)]
#print(parms[4], confdic.get('accur', aligner.ACCUR_CHOICE[0]), type(parms[4]))
# check the user-inputs
old="""
try:
parms[3] = float(parms[3])
except ValueError:
G.openMsg(parent=self, msg='The default value (%.2f um) will be used' % af.MAX_SHIFT, title="The value for max shift allowed is missing")
parms[3] = af.MAX_SHIFT
self.maxShift.SetValue(str(parms[3]))"""
if not parms[6]:
G.openMsg(parent=self, msg='The default suffix will be used', title="The file suffix is missing")
parms[6] = aligner.IMG_SUFFIX
self.img_suffix_txt.SetValue(parms[6])
# save current settings
C.saveConfig(cutout=parms[0], local=parms[2], accur=parms[4], parm_suffix_txt=parms[5], img_suffix_txt=parms[6], format=parms[8], min_pxls_yx=parms[9])
#C.saveConfig(cutout=parms[0], local=parms[2], maxShift=parms[3], accur=parms[4], parm_suffix_txt=parms[5], img_suffix_txt=parms[6], format=parms[8], min_pxls_yx=parms[9])
# run program
gui = threads.GUImanager(self, __name__)
self.th = threads.ThreadWithExc(gui, self.localChoice, fns, targets, parms)
self.th.start()
else:
tid = self.th._get_my_tid()
threads.async_raise(tid, threads.MyError)
def _setInitGuess(self, fn):
self.initGuess.clearAll()
self.initGuess.addFile(fn)
self.clearInitguessButton.Enable(1)
C.saveConfig(initguess=fn)
def OnGo(self, ev=None):
"""
run or cancel the alignment program
The actual sequence of processes is written in threads.ThreadWithExc.run()
"""
if self.goButton.GetValue():
if not self.listRef.columnkeys:
return
fns = [
os.path.join(*self.listRef.getFile(index)[:2])
for index in self.listRef.columnkeys
]
targets = [
os.path.join(*self.listTgt.getFile(index)[:2])
for index in self.listTgt.columnkeys
]
# other parameters
initguess = ''
form = self.outextch.GetStringSelection()
if not form:
G.openMsg(
parent=self,
msg=
'Please select the output file format next to the Suffix text box',
title="The format type is missing")
self.goButton.SetValue(0)
return
parms = [
self.cutoutCb.GetValue(),
initguess,
self.localListChoice.GetStringSelection(),
self.maxShift.GetValue(),
self.zmagch.GetStringSelection(),
self.parm_suffix_txt.GetValue(),
self.img_suffix_txt.GetValue(),
[nt for nt in self.listRef.nts], # copy
form,
int(self.min_pxls_choice.GetStringSelection())
]
# check the user-inputs
try:
parms[3] = float(parms[3])
except ValueError:
G.openMsg(parent=self,
msg='The default value (%.2f um) will be used' %
af.MAX_SHIFT,
title="The value for max shift allowed is missing")
parms[3] = af.MAX_SHIFT
self.maxShift.SetValue(str(parms[3]))
if not parms[6]:
G.openMsg(parent=self,
msg='The default suffix will be used',
title="The file suffix is missing")
parms[6] = alginer.IMG_SUFFIX
self.img_suffix_txt.SetValue(parms[6])
# save current settings
C.saveConfig(cutout=parms[0],
local=parms[2],
maxShift=parms[3],
Zmag=parms[4],
parm_suffix_txt=parms[5],
img_suffix_txt=parms[6],
format=parms[8],
min_pxls_yx=parms[9])
# run program
gui = threads.GUImanager(self, __name__)
self.th = threads.ThreadWithExc(gui, self.localChoice, fns,
targets, parms)
self.th.start()
else:
tid = self.th._get_my_tid()
threads.async_raise(tid, threads.MyError)
def _setInitGuess(self, fn):
self.initGuess.clearAll()
self.initGuess.addFile(fn)
self.clearInitguessButton.Enable(1)
C.saveConfig(initguess=fn)
