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 OnOutFormatChosen(self, evt=None):
outext = self.outextch.GetStringSelection()
if outext == self.outext_choices[-1] and not imgio.bioformatsIO.HAS_JDK:
listbox.imgio_dialog('Writing the file format (%s) requres Java Development Kit (JDK)' % outext)
confdic = C.readConfig()
outext = confdic.get('format', aligner.WRITABLE_FORMATS[0])
self.outextch.SetStringSelection(outext)
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 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 OnOutFormatChosen(self, evt=None):
outext = self.outextch.GetStringSelection()
if outext == self.outext_choices[-1] and not imgio.bioformatsIO.HAS_JDK:
listbox.imgio_dialog(
'Writing the file format (%s) requres Java Development Kit (JDK)'
% outext)
confdic = C.readConfig()
outext = confdic.get('format', aligner.WRITABLE_FORMATS[0])
self.outextch.SetStringSelection(outext)
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 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 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 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 makePanel(self):
# config
confdic = C.readConfig()
self.lastpath = confdic.get('lastpath', '')
self.extra_parms = {}
# draw / arrange
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# ---- reference ------
# \n
box = G.newSpaceV(sizer)
self.refAddButton = G.makeButton(self, box, lambda ev:self.OnChooseImgFiles(ev,'ref'), title='Reference files', tip='', enable=True)
self.refClearButton = G.makeButton(self, box, lambda ev:self.clearSelected(ev, 'ref'), title='Clear selected', tip='', enable=False)
parmSuffixLabel, self.parm_suffix_txt = G.makeTxtBox(self, box, 'Suffix', defValue=confdic.get('parm_suffix_txt', ''), tip='A suffix for the file extention for the chromagnon file name', sizeX=100)
extraButton = G.makeButton(self, box, self.OnExtraParamButton, title='Extra parameters')
# ---- target ------
refsize = self.refAddButton.GetSize()[0] + self.refClearButton.GetSize()[0] + parmSuffixLabel.GetSize()[0] + self.parm_suffix_txt.GetSize()[0] + extraButton.GetSize()[0]
G.newSpaceH(box, LISTSIZE_X+LISTSPACE-refsize)
self.tgtAddButton = G.makeButton(self, box, lambda ev:self.OnChooseImgFiles(ev,'target'), title='Target files', tip='', enable=True)
self.tgtClearButton = G.makeButton(self, box, lambda ev:self.clearSelected(ev, 'tareget'), title='Clear selected', tip='', enable=False)
self.cutoutCb = G.makeCheck(self, box, "crop margins", tip='', defChecked=bool(confdic.get('cutout', True)))
label, self.img_suffix_txt = G.makeTxtBox(self, box, 'Suffix', defValue=confdic.get('img_suffix_txt', aligner.IMG_SUFFIX), tip='A suffix for the file name', sizeX=100)
self.outext_choices = [os.path.extsep + form for form in aligner.WRITABLE_FORMATS]
label, self.outextch = G.makeListChoice(self, box, '', self.outext_choices, defValue=confdic.get('format', aligner.WRITABLE_FORMATS[0]), tip='tif: ImageJ format, dv: DeltaVision format, ome.tif: OME-tif format (slow)', targetFunc=self.OnOutFormatChosen)
if not self.outextch.GetStringSelection():
self.outextch.SetSelection(0)
## --- list ----
# \n
box = G.newSpaceV(sizer)
self.listRef = listbox.FileListCtrl(self, wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE,
#| wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y)
)
box.Add(self.listRef)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, lambda ev:self.OnItemSelected(ev, 'reference'), self.listRef)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.listRef)
self.listRef.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
G.newSpaceH(box, LISTSPACE)
self.listTgt = listbox.FileListCtrl(self, wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE,
# | wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y)
)
box.Add(self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, lambda ev:self.OnItemSelected(ev, 'target'), self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.listTgt)
self.listTgt.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
self.listRef.setDefaultFileLoadFunc(self._load_func)
self.listTgt.setDefaultFileLoadFunc(self._load_func)
#------- execute ------
# \n
box = G.newSpaceV(sizer)
self.goButton = G.makeToggleButton(self, box, self.OnGo, title='Run all', tip='', enable=False)
if sys.platform.startswith('win'):
ft = wx.Font(9, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
elif sys.platform.startswith('linux'):
ft = wx.Font(11, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
else:
ft = wx.Font(14, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
self.goButton.SetFont(ft)
self.listRef.setOnDrop(self.goButton.Enable, 1)
self.listTgt.setOnDrop(self.goButton.Enable, 1)
self.averageCb = G.makeCheck(self, box, "average references ", tip='Multiple reference images are maximum intensity projected to make a single high SNR image for shift calculation.', defChecked=bool(confdic.get('average', False)))
self.localChoice = LOCAL_CHOICE
label, self.localListChoice = G.makeListChoice(self, box, 'Local align', self.localChoice, defValue=confdic.get('local', 'None'), targetFunc=self.OnLocalListChose)
self.min_pxls_label, self.min_pxls_choice = G.makeListChoice(self, box, 'min window size', af.MIN_PXLS_YXS, defValue=confdic.get('min_pxls_yx', af.MIN_PXLS_YXS[1]), tip='Minimum number of pixel to divide as elements of local alignment')
self.OnLocalListChose()
self.progress = wx.Gauge(self, -1, 100, size=(100,-1))
box.Add(self.progress)
self.label = G.makeTxt(self, box, ' ')
_col_sizes=[(key, val) for key, val in listbox.__dict__.items() if key.startswith('SIZE_COL')]
_col_sizes.sort()
LISTSIZE_X2 = sum([val for key, val in _col_sizes[:3]])
LIST_Y2 = 30
#------ flat fielder --------
self.flatButton = wx.Button(self, -1, 'Open Flat Fielder')
self.flatButton.SetToolTip(wx.ToolTip('Open a graphical interphase to flat field images'))
flatsize = self.goButton.GetSize()[0] + self.averageCb.GetSize()[0] + label.GetSize()[0] + self.localListChoice.GetSize()[0] + self.min_pxls_label.GetSize()[0] + self.min_pxls_choice.GetSize()[0] + self.progress.GetSize()[0] + self.flatButton.GetSize()[0] + 5
G.newSpaceH(box, FRAMESIZE_X-flatsize)
box.Add(self.flatButton)
frame = self.GetTopLevelParent()
frame.Bind(wx.EVT_BUTTON, self.onFlatFielder, self.flatButton)
# ----- finishing -----
self.Layout()
self.parent.Layout()
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 makePanel(self, tif=False):
# config
confdic = C.readConfig()
self.lastpath = confdic.get('lastpath', '')
# draw / arrange
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# ---- reference ------
# \n
box = G.newSpaceV(sizer)
self.refAddButton = G.makeButton(
self,
box,
lambda ev: self.OnChooseImgFiles(ev, 'ref'),
title='Reference files',
tip='',
enable=True)
self.refClearButton = G.makeButton(
self,
box,
lambda ev: self.clearSelected(ev, 'ref'),
title='Clear selected',
tip='',
enable=False)
maxShiftLabel, self.maxShift = G.makeTxtBox(
self,
box,
'max shift allowed (um)',
defValue=confdic.get('maxShift', af.MAX_SHIFT),
tip='maximum possible shift of each channel',
sizeX=50)
parmSuffixLabel, self.parm_suffix_txt = G.makeTxtBox(
self,
box,
'Suffix',
defValue=confdic.get('parm_suffix_txt', ''),
tip='A suffix for the file extention for the chromagnon file name',
sizeX=100)
#self.refwave = G.makeButton(self, box, lambda ev:self.clearSelected(ev, 'ref'), title='Ref channel', tip='', enable=True)
# ---- target ------
refsize = self.refAddButton.GetSize()[0] + self.refClearButton.GetSize(
)[0] + parmSuffixLabel.GetSize()[0] + self.parm_suffix_txt.GetSize(
)[0] + maxShiftLabel.GetSize()[0] + self.maxShift.GetSize()[0]
G.newSpaceH(box, LISTSIZE_X + LISTSPACE - refsize)
self.tgtAddButton = G.makeButton(
self,
box,
lambda ev: self.OnChooseImgFiles(ev, 'target'),
title='Target files',
tip='',
enable=True)
self.tgtClearButton = G.makeButton(
self,
box,
lambda ev: self.clearSelected(ev, 'tareget'),
title='Clear selected',
tip='',
enable=False)
self.cutoutCb = G.makeCheck(self,
box,
"crop margins",
tip='',
defChecked=bool(confdic.get(
'cutout', True)))
label, self.img_suffix_txt = G.makeTxtBox(
self,
box,
'Suffix',
defValue=confdic.get('img_suffix_txt', aligner.IMG_SUFFIX),
tip='A suffix for the file name',
sizeX=100)
self.outext_choices = [
os.path.extsep + form for form in aligner.WRITABLE_FORMATS
]
label, self.outextch = G.makeListChoice(
self,
box,
'',
self.outext_choices,
defValue=confdic.get('format', aligner.WRITABLE_FORMATS[0]),
tip=
'tif: ImageJ format, dv: DeltaVision format, ome.tif: OME-tif format (slow)',
targetFunc=self.OnOutFormatChosen)
if not self.outextch.GetStringSelection():
self.outextch.SetSelection(0)
## --- list ----
# \n
box = G.newSpaceV(sizer)
self.listRef = listbox.FileListCtrl(
self,
wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE,
#| wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y))
box.Add(self.listRef)
self.Bind(wx.EVT_LIST_ITEM_SELECTED,
lambda ev: self.OnItemSelected(ev, 'reference'),
self.listRef)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected,
self.listRef)
self.listRef.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
G.newSpaceH(box, LISTSPACE)
self.listTgt = listbox.FileListCtrl(
self,
wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE,
# | wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y))
box.Add(self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_SELECTED,
lambda ev: self.OnItemSelected(ev, 'target'), self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected,
self.listTgt)
self.listTgt.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
self.listRef.setDefaultFileLoadFunc(self._load_func)
self.listTgt.setDefaultFileLoadFunc(self._load_func)
#------- execute ------
# \n
box = G.newSpaceV(sizer)
self.goButton = G.makeToggleButton(self,
box,
self.OnGo,
title='Run all',
tip='',
enable=False)
if sys.platform.startswith('win'):
ft = wx.Font(9, wx.FONTFAMILY_DEFAULT, wx.NORMAL,
wx.FONTWEIGHT_BOLD)
elif sys.platform.startswith('linux'):
ft = wx.Font(11, wx.FONTFAMILY_DEFAULT, wx.NORMAL,
wx.FONTWEIGHT_BOLD)
else:
ft = wx.Font(14, wx.FONTFAMILY_DEFAULT, wx.NORMAL,
wx.FONTWEIGHT_BOLD)
self.goButton.SetFont(ft)
self.listRef.setOnDrop(self.goButton.Enable, 1)
self.listTgt.setOnDrop(self.goButton.Enable, 1)
self.zmaglabel, self.zmagch = G.makeListChoice(
self,
box,
' Z mag',
aligner.ZMAG_CHOICE,
defValue=confdic.get('Zmag', aligner.ZMAG_CHOICE[0]),
tip=
'if "Auto" is chosen, then z mag calculation is done if the z stack contains more than 30 Z sections with a sufficient contrast'
)
self.localChoice = LOCAL_CHOICE
label, self.localListChoice = G.makeListChoice(
self,
box,
'Local align',
self.localChoice,
defValue=confdic.get('local', 'None'),
targetFunc=self.OnLocalListChose)
self.min_pxls_label, self.min_pxls_choice = G.makeListChoice(
self,
box,
'min window size',
af.MIN_PXLS_YXS,
defValue=confdic.get('min_pxls_yx', af.MIN_PXLS_YXS[1]),
tip=
'Minimum number of pixel to divide as elements of local alignment')
self.OnLocalListChose()
self.progress = wx.Gauge(self, -1, 100, size=(100, -1))
box.Add(self.progress)
self.label = G.makeTxt(self, box, ' ')
_col_sizes = [(key, val) for key, val in listbox.__dict__.items()
if key.startswith('SIZE_COL')]
_col_sizes.sort()
LISTSIZE_X2 = sum([val for key, val in _col_sizes[:3]])
LIST_Y2 = 30
#------ flat fielder --------
self.flatButton = wx.Button(self, -1, 'Open Flat Fielder')
self.flatButton.SetToolTip(
wx.ToolTip('Open a graphical interphase to flat field images'))
flatsize = self.goButton.GetSize()[0] + self.zmaglabel.GetSize(
)[0] + self.zmagch.GetSize()[0] + label.GetSize(
)[0] + self.localListChoice.GetSize()[0] + self.min_pxls_label.GetSize(
)[0] + self.min_pxls_choice.GetSize()[0] + self.progress.GetSize(
)[0] + self.flatButton.GetSize()[0] + 5
G.newSpaceH(box, FRAMESIZE_X - flatsize)
box.Add(self.flatButton)
frame = self.GetTopLevelParent()
frame.Bind(wx.EVT_BUTTON, self.onFlatFielder, self.flatButton)
# ----- finishing -----
self.Layout()
self.parent.Layout()
self.checkGo()
def makePanel(self, tif=False):
# config
confdic = C.readConfig()
self.lastpath = confdic.get('lastpath', '')
# draw / arrange
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# ---- reference ------
# \n
box = G.newSpaceV(sizer)
self.refAddButton = G.makeButton(self, box, self.OnChooseReferenceFile, title='Reference file', tip='', enable=True)
self.refClearButton = G.makeButton(self, box, lambda ev:self.clearSelected(ev, 'ref'), title='Clear selected', tip='', enable=False)
flatSuffixLabel, self.flat_suffix_txt = G.makeTxtBox(self, box, 'Suffix', defValue=confdic.get('flat_suffix_txt', ''), tip='A suffix before the file extention for the .flat file name', sizeX=100)
#------- execute ------
self.goButton = wx.ToggleButton(self, -1, 'Run all')
if sys.platform.startswith('win'):
ft = wx.Font(9, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
elif sys.platform.startswith('linux'):
ft = wx.Font(11, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
else:
ft = wx.Font(14, wx.FONTFAMILY_DEFAULT, wx.NORMAL, wx.FONTWEIGHT_BOLD)
self.goButton.SetFont(ft)
#self.goButton.SetToolTipString('Open a graphical interphase to flat field images')
gosize = self.refAddButton.GetSize()[0] + self.refClearButton.GetSize()[0] + self.goButton.GetSize()[0] + flatSuffixLabel.GetSize()[0] + self.flat_suffix_txt.GetSize()[0]
G.newSpaceH(box, LISTSIZE_X-gosize)
box.Add(self.goButton)
frame = self.GetTopLevelParent()
frame.Bind(wx.EVT_TOGGLEBUTTON, self.OnGo, self.goButton)
## --- list reference ----
# \n
box = G.newSpaceV(sizer)
self.listRef = listbox.FileListCtrl(self, wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE
| wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y2),
multiple=False)
box.Add(self.listRef)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, lambda ev:self.OnItemSelected(ev, 'reference'), self.listRef)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.listRef)
self.listRef.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
flatfn = confdic.get('flatfn', '_FLAT')
if os.path.isfile(flatfn):
self.listRef.addFile(flatfn)
self.listRef.setDefaultFileLoadFunc(self._load_func)
# ---- list target ------
# \n
box = G.newSpaceV(sizer)
self.tgtAddButton = G.makeButton(self, box, self.OnChooseTargetFiles, title='Target files', tip='', enable=True)
self.tgtClearButton = G.makeButton(self, box, lambda ev:self.clearSelected(ev, 'tareget'), title='Clear selected', tip='', enable=False)
label, self.flatimg_suffix_txt = G.makeTxtBox(self, box, 'Suffix', defValue=confdic.get('flatimg_suffix_txt', '_'+flatConv.EXT.upper()), tip='A suffix for the output file name', sizeX=100)
choices = [os.path.extsep + form for form in aligner.WRITABLE_FORMATS]
label, self.outextch = G.makeListChoice(self, box, '', choices, defValue=confdic.get('flat_format', aligner.WRITABLE_FORMATS[0]), tip='Choose image file formats; for reading with ImageJ, dv is recommended.')
# \n
box = G.newSpaceV(sizer)
self.listTgt = listbox.FileListCtrl(self, wx.NewId(),
style=wx.LC_REPORT
| wx.BORDER_NONE
| wx.LC_SORT_ASCENDING,
size=(LISTSIZE_X, LIST_Y)
)
box.Add(self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, lambda ev:self.OnItemSelected(ev, 'target'), self.listTgt)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.listTgt)
self.listTgt.Bind(wx.EVT_LEFT_DCLICK, self.OnDoubleClick)
self.listTgt.setDefaultFileLoadFunc(self._load_func)
# ---- Drop befavior ----
self.listRef.setOnDrop(self.checkGo, 1)#goButton.Enable, 1)
self.listTgt.setOnDrop(self.checkGo, 1)#goButton.Enable, 1)
# ---- Output ------
# \n
box = G.newSpaceV(sizer)
self.label = G.makeTxt(self, box, ' ')
# ----- finishing -----
self.Layout()
#self.parent.Layout()
self.checkGo()
