def __init__(self, parent):
sizeX = parent.GetSize()[0] - parent.cpanel.clist.GetSize()[0]
wx.Panel.__init__(self, parent, -1, size=(sizeX, -1))
#self.parent = parent
# start drawing
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# \n
box = G.newSpaceV(sizer)
G.makeTxt(
self, box,
'Drag and drop a file to preview the parameters\n or click the button to select a file'
)
# \n
box = G.newSpaceV(sizer)
self.testButton = G.makeButton(self,
box,
self.onChooseFile,
title='Open')
dropTarget = ViewFileDropTarget(self)
self.SetDropTarget(dropTarget)
def __init__(self, parent):
sizeX = parent.GetSize()[0] - parent.cpanel.clist.GetSize()[0]
wx.Panel.__init__(self, parent, -1, size=(sizeX,-1))
#self.parent = parent
# start drawing
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, 'Drag and drop a file to preview the parameters\n or click the button to select a file')
# \n
box = G.newSpaceV(sizer)
self.testButton = G.makeButton(self, box, self.onChooseFile, title='Open')
dropTarget = ViewFileDropTarget(self)
self.SetDropTarget(dropTarget)
def initHists(self):
''' Initialize the histogram/aligner panel, and a bunch of empty lists;
define HistogramCanvas class;s doOnBrace() and doOnMouse() behaviors
'''
self.histsPanel = scrolled.ScrolledPanel(self, -1)#wx.Panel(self, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
self.histsPanel.SetSizer(sizer)
cookiecutterSizer = wx.BoxSizer(wx.HORIZONTAL)
# This sizer contains both the cookie cutter toggle button and the cropbox editor
sizer.Add(cookiecutterSizer, 0, wx.ALL|wx.EXPAND, 2)
autoscaleButton = G.makeButton(self.histsPanel, cookiecutterSizer, self.OnAutoScale, title='Auto scale', tip='')
self.hist = [None] * self.doc.nw
self.hist_arr = [None] * self.doc.nw
self.hist_min = [None]*self.doc.nw
self.hist_max = [None]*self.doc.nw
self.hist_toggleButton = [None]*self.doc.nw
self.hist_show = [None]*self.doc.nw
self.mmms = [None]*self.doc.nw
self.intensity_label = [None] * self.doc.nw
self.hist_label = [None] * self.doc.nw
self.hist_singleChannelMode = None
self.hist_toggleID2col = {}
for i in range(self.doc.nw):
wave = self.doc.wave[i]#mrcIO.getWaveFromHdr(self.doc.hdr, i)
self.hist_show[i] = True
box = G.newSpaceV(sizer)
self.hist_toggleButton[i] = G.makeToggleButton(self.histsPanel, box, self.OnHistToggleButton, title=str(wave), size=(40,-1))
self.hist_toggleButton[i].Bind(wx.EVT_RIGHT_DOWN,
lambda ev: self.OnHistToggleButton(ev, i=i, mode="r"))
self.hist_toggleButton[i].SetValue( self.hist_show[i] )
self.intensity_label[i] = G.makeTxt(self.histsPanel, box, ' ')
box = G.newSpaceV(sizer)
self.hist[i] = histogram.HistogramCanvas(self.histsPanel, size=(200,30))#size)
box.Add(self.hist[i])
for ii,colName in enumerate(_rgbList_names):
self.hist[i].menu.Insert(ii, _rgbList_menuIDs[ii], colName)
self.hist[i].Bind(wx.EVT_MENU, self.OnHistColorChange, id=_rgbList_menuIDs[ii])
self.hist[i].menu.InsertSeparator(ii+1)
self.hist_toggleID2col[ self.hist_toggleButton[i].GetId() ] = i
#/n
box = G.newSpaceV(sizer)
self.hist_label[i] = G.makeTxt(self.histsPanel, box, ' ')
def fff(s, ii=i):
l, r = s.leftBrace, s.rightBrace
for v in self.viewers:
## TODO: different scaling for x-z and y-z viewer??
v.changeHistScale(ii, l, r)
self.hist[i].doOnBrace.append(fff)
def ggg(xEff, ev, ii=i):
l,r = self.hist[ii].leftBrace, self.hist[ii].rightBrace
if self.doc.dtype in (N.uint8, N.int16, N.uint16, N.int32):
self.hist_label[ii].SetLabel("I: %6.0f l/r: %6.0f %6.0f" %(xEff,l,r))
else:
self.hist_label[ii].SetLabel("I: %7.1f l/r: %7.1f %7.1f" %(xEff,l,r))
self.hist[i].doOnMouse.append(ggg)
if self.doc.nw > 1:
for i in range(self.doc.nw):
wave = self.doc.wave[i]
self.setColor(i, wave, False)
#/n/n
box = G.newSpaceV(sizer)
G.makeTxt(self.histsPanel, box, ' ') # dummy
box = G.newSpaceV(sizer)
self.xy_label = G.makeTxt(self.histsPanel, box, ' ')
self.histsPanel.SetAutoLayout(1)
self.histsPanel.SetupScrolling()
def addZslider(self):
self.sliderPanel = wx.Panel(self, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
self.sliderPanel.SetSizer(sizer)
# image info
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self.sliderPanel, box, title='Image info', size=wx.DefaultSize)
if sys.platform.startswith(('win', 'linux')):
fsize = 9
else:
fsize = 11
font = wx.Font(fsize, wx.SWISS, wx.NORMAL, wx.NORMAL)
# pixel size
pxsiz = tuple(self.doc.pxlsiz[::-1])
dimstr = ('X', 'Y', 'Z')
line = 'Pixel size (um):\n'
pxstr = ' '
for i, d in enumerate(pxsiz):
if d:
pxstr += '%s %.3f: ' % (dimstr[i], d)
if pxstr:
line += pxstr[:-2]
else:
line = ''
if line:
label = G.makeTxt(self.sliderPanel, box, line)
label.SetFont(font)
# data type
pxtype = imgio.bioformatsIO.pixeltype_to_bioformats(self.doc.dtype)
line = 'Data type: %s' % pxtype
label = G.makeTxt(self.sliderPanel, box, line)
label.SetFont(font)
# z slider
if self.doc.nz > 1:
topSizer = G.newSpaceV(sizer)
#label, self.zSliderBox = G.makeTxtBox(self.sliderPanel, topSizer, 'Z', defValue=str(self.doc.z), tip='enter z idx', style=wx.TE_PROCESS_ENTER)
label, self.zSliderBox = G.makeTxtBox(self.sliderPanel, topSizer, 'Z', defValue=self.doc.z, tip='enter z idx', style=wx.TE_PROCESS_ENTER)
self.zSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnZSliderBox)
G.makeTxt(self.sliderPanel, topSizer, r'/'+str(self.doc.nz-1))
self.zSlider = wx.Slider(self.sliderPanel, wx.ID_ANY, self.doc.z, 0,
self.doc.nz-1,
size=wx.Size(150,-1),
style = wx.SL_HORIZONTAL | wx.SL_AUTOTICKS)#|wx.SL_LABELS | wx.SL_AUTOTICKS)
topSizer.Add(self.zSlider, 6, wx.ALL|wx.ALIGN_LEFT, 2)
#wx.EVT_SLIDER(self, self.zSlider.GetId(), self.OnZSlider)
self.Bind(wx.EVT_SLIDER, self.OnZSlider, id=self.zSlider.GetId())
#wx.EVT_KEY_DOWN(self, self.zSlider.GetId(), self.OnKeyZSlider)
#self.zSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
if self.doc.nt == 1:
self.sliderPanel.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
self.zSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
#self.Bind(wx.EVT_CHAR, self.OnKeyZSlider)
#/n
box = G.newSpaceV(sizer)
autofocusButton = G.makeButton(self.sliderPanel, box, self.OnAutoFocus, title='Auto focus', tip='')
#/n
box = G.newSpaceV(sizer)
self.orthogonal_toggle = G.makeToggleButton(self.sliderPanel, box, self.onOrthogonal, title='Orthogonal projections')
#/n
box = G.newSpaceV(sizer)
self.saveScrButton = G.makeButton(self.sliderPanel, box, self.onSaveScr, title='Save screen')
self.choice_viewers = ['XY', 'XZ', 'ZY']
label, self.viewerch = G.makeListChoice(self.sliderPanel, box, 'viewer', self.choice_viewers, defValue=[self.choice_viewers[0]])
self.viewerch.Enable(0)
# t slider
if self.doc.nt > 1: ## need a time slider
box = G.newSpaceV(sizer)
label, self.tSliderBox = G.makeTxtBox(self.sliderPanel, box, 'T', defValue=str(self.doc.t), tip='enter time idx', style=wx.TE_PROCESS_ENTER)
self.tSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnTSliderBox)
G.makeTxt(self.sliderPanel, box, r'/'+str(self.doc.nt-1))
self.tSlider = wx.Slider(self.sliderPanel, wx.ID_ANY, 0, 0,
self.doc.nt-1,
size=wx.Size(150,-1),
style = wx.SL_HORIZONTAL | wx.SL_AUTOTICKS)#|wx.SL_LABELS | wx.SL_AUTOTICKS)
box.Add(self.tSlider, 6, wx.ALL|wx.ALIGN_LEFT, 2)
#wx.EVT_SLIDER(self, self.tSlider.GetId(), self.OnTSlider)
self.Bind(wx.EVT_SLIDER, self.OnTSlider, id=self.tSlider.GetId())
if self.doc.nz == 1:
self.sliderPanel.Bind(wx.EVT_KEY_DOWN, self.OnKeyTSlider)
self.tSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyTSlider)
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 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 __init__(self, parent=None, fns=[], defPxlSiz=0.1):
"""
dimension selection dialog for multipage tif
fns: filenames
use like
>>> dlg = FileSelectorDialog()
>>> if dlg.ShowModal() == wx.ID_OK:
>>> fns = dlg.GetPaths()
"""
wx.Dialog.__init__(self, parent, -1, title='Image Dimensions')
nfns = len(fns)
sizer = wx.BoxSizer(wx.VERTICAL)
hsz = wx.FlexGridSizer(nfns + 1, 14, 0, 0)
sizer.Add(hsz, 0, wx.EXPAND)
# header
G.makeTxt(self, hsz, 'Directory')
G.makeTxt(self, hsz, 'Filename')
G.makeTxt(self, hsz, 'Sequence')
G.makeTxt(self, hsz, 'time')
G.makeTxt(self, hsz, ' color: ')
for i, col in enumerate(_COLORS):
b = G.makeTxt(self, hsz, col)
b.SetForegroundColour(_COLOR_NAME[i])
G.makeTxt(self, hsz, ' Z')
G.makeTxt(self, hsz, 'Pixel size (um)')
# file
self.holders = []
for fn in fns:
h = DimDataHolder(fn, defPxlSiz)
self.holders.append(h)
G.makeTxt(self, hsz, h.direc)
G.makeTxt(self, hsz, h.basename)
label, h.seqChoice = G.makeListChoice(
self,
hsz,
'',
generalIO.IMGSEQ,
defValue=h.seq,
targetFunc=self.onSeq
) #imgfileIO.generalIO.IMGSEQ[h.seq], targetFunc=self.onSeq)
comm_divs = [
str(i) for i in range(1, h.nsec + 1) if not h.nsec % i
]
label, h.ntChoice = G.makeListChoice(self,
hsz,
'',
comm_divs,
defValue=h.nt,
targetFunc=self.onNumTimes)
G.makeTxt(self, hsz, '')
defcols = [_COLORS[_WAVES.index(w)] for w in h.waves]
h.nwChecks = [
G.makeCheck(self,
hsz,
"",
defChecked=(col in defcols),
targetFunc=self.onWaves) for col in _COLORS
]
h.nzlabel = G.makeTxt(self,
hsz,
str(int(h.getZ())),
flag=wx.ALIGN_RIGHT)
h.pxlsiz_txt = wx.TextCtrl(self,
-1,
'%.2f' % h.pxlsiz,
size=(50, -1))
hsz.Add(h.pxlsiz_txt)
#label, self.pxlsiz_txt = G.makeTxtBox(self, hsz, '', '0.10', tip='The size of a pixel after magnification', sizeX=50)
wx.EVT_TEXT(self, h.pxlsiz_txt.GetId(), self.onPxlSiz)
bsz = wx.StdDialogButtonSizer()
sizer.Add(bsz, 0, wx.EXPAND)
button = wx.Button(self, wx.ID_CANCEL)
bsz.AddButton(button)
self.okbutton = wx.Button(self, wx.ID_OK)
bsz.AddButton(self.okbutton)
bsz.Realize()
self.SetSizer(sizer)
sizer.Fit(self)
def __init__(self, parent, fn):
"""
fn: a chromagnon file
"""
wx.Panel.__init__(self, parent, -1)
self.clist = ChromagnonList(self, fn)
self.fn = fn
# start drawing
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, fn)
# \n
box = G.newSpaceV(sizer)
if self.clist.map_str != 'None':
G.makeTxt(self, box, 'Local: ')
self.local_label = G.makeTxt(self, box, self.clist.map_str)
self.viewLocalButton = G.makeButton(
self,
box,
self.onViewLocal,
title='View',
tip='View local distortion as a image')
# \n
box = G.newSpaceV(sizer)
G.makeTxt(
self, box,
"The file is a .ome.tif file, and the alignment parameters are stored in it's metadata."
)
else:
# \n
box = G.newSpaceV(sizer)
G.makeTxt(
self, box,
'The file is a text file: rename to ".csv" to open as a spread sheet.'
)
# \n\n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, ' ')
box = G.newSpaceV(sizer)
G.makeTxt(
self, box, 'Pixel size ZYX (um): %.3f %.3f %.3f' %
tuple(self.clist.creader.pxlsiz))
if self.clist.nt > 1:
# \n
box = G.newSpaceV(sizer)
label, self.tSliderBox = G.makeTxtBox(self,
box,
'T',
defValue=str(self.clist.t),
tip='enter time idx',
style=wx.TE_PROCESS_ENTER)
self.tSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnTSliderBox)
G.makeTxt(self, box, r'/' + str(self.clist.nt - 1))
self.tSlider = wx.Slider(self,
wx.ID_ANY,
0,
0,
self.clist.nt - 1,
size=wx.Size(150, -1),
style=wx.SL_HORIZONTAL | wx.SL_AUTOTICKS)
box.Add(self.tSlider, 6, wx.ALL | wx.ALIGN_LEFT, 2)
wx.EVT_SLIDER(self, self.tSlider.GetId(), self.OnTSlider)
# \n
box = G.newSpaceV(sizer)
box.Add(self.clist)
# \n
box = G.newSpaceV(sizer)
self.saveButton = G.makeButton(
self,
box,
self.onSave,
title='Save as...',
tip='Save editted parameter into a chromagnon file'
) #, enable=False)
#self.exportButton = G.makeButton(self, box, self.onExport, title='Export as .csv', tip='Save editted parameter into a comma separated file')
self.clearButton = G.makeButton(self,
box,
self.clearSelected,
title='Remove selected',
tip='Remove one wavelength')
self.addButton = G.makeButton(self,
box,
self.addRow,
title='add wavelength',
tip='Add one wavelength')
self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.clist)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.clist)
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()
def initHists(self):
''' Initialize the histogram/aligner panel, and a bunch of empty lists;
define HistogramCanvas class;s doOnBrace() and doOnMouse() behaviors
'''
self.histsPanel = scrolled.ScrolledPanel(self, -1) #wx.Panel(self, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
self.histsPanel.SetSizer(sizer)
cookiecutterSizer = wx.BoxSizer(wx.HORIZONTAL)
# This sizer contains both the cookie cutter toggle button and the cropbox editor
sizer.Add(cookiecutterSizer, 0, wx.ALL | wx.EXPAND, 2)
autoscaleButton = G.makeButton(self.histsPanel,
cookiecutterSizer,
self.OnAutoScale,
title='Auto scale',
tip='')
self.hist = [None] * self.doc.nw
self.hist_arr = [None] * self.doc.nw
self.hist_min = [None] * self.doc.nw
self.hist_max = [None] * self.doc.nw
self.hist_toggleButton = [None] * self.doc.nw
self.hist_show = [None] * self.doc.nw
self.mmms = [None] * self.doc.nw
self.intensity_label = [None] * self.doc.nw
self.hist_label = [None] * self.doc.nw
self.hist_singleChannelMode = None
self.hist_toggleID2col = {}
for i in range(self.doc.nw):
wave = self.doc.wave[i] #mrcIO.getWaveFromHdr(self.doc.hdr, i)
self.hist_show[i] = True
box = G.newSpaceV(sizer)
self.hist_toggleButton[i] = G.makeToggleButton(
self.histsPanel,
box,
self.OnHistToggleButton,
title=str(wave),
size=(40, -1))
self.hist_toggleButton[i].Bind(
wx.EVT_RIGHT_DOWN,
lambda ev: self.OnHistToggleButton(ev, i=i, mode="r"))
self.hist_toggleButton[i].SetValue(self.hist_show[i])
self.intensity_label[i] = G.makeTxt(self.histsPanel, box, ' ')
box = G.newSpaceV(sizer)
self.hist[i] = histogram.HistogramCanvas(self.histsPanel,
size=(200, 30)) #size)
box.Add(self.hist[i])
for ii, colName in enumerate(_rgbList_names):
self.hist[i].menu.Insert(ii, _rgbList_menuIDs[ii], colName)
self.hist[i].Bind(wx.EVT_MENU,
self.OnHistColorChange,
id=_rgbList_menuIDs[ii])
self.hist[i].menu.InsertSeparator(ii + 1)
self.hist_toggleID2col[self.hist_toggleButton[i].GetId()] = i
#/n
box = G.newSpaceV(sizer)
self.hist_label[i] = G.makeTxt(self.histsPanel, box, ' ')
def fff(s, ii=i):
l, r = s.leftBrace, s.rightBrace
for v in self.viewers:
## TODO: different scaling for x-z and y-z viewer??
v.changeHistScale(ii, l, r)
self.hist[i].doOnBrace.append(fff)
def ggg(xEff, ev, ii=i):
l, r = self.hist[ii].leftBrace, self.hist[ii].rightBrace
if self.doc.dtype in (N.uint8, N.int16, N.uint16, N.int32):
self.hist_label[ii].SetLabel("I: %6.0f l/r: %6.0f %6.0f" %
(xEff, l, r))
else:
self.hist_label[ii].SetLabel("I: %7.1f l/r: %7.1f %7.1f" %
(xEff, l, r))
self.hist[i].doOnMouse.append(ggg)
if self.doc.nw > 1:
for i in range(self.doc.nw):
wave = self.doc.wave[i]
self.setColor(i, wave, False)
#/n/n
box = G.newSpaceV(sizer)
G.makeTxt(self.histsPanel, box, ' ') # dummy
box = G.newSpaceV(sizer)
self.xy_label = G.makeTxt(self.histsPanel, box, ' ')
self.histsPanel.SetAutoLayout(1)
self.histsPanel.SetupScrolling()
def addZslider(self):
self.sliderPanel = wx.Panel(self, -1)
sizer = wx.BoxSizer(wx.VERTICAL)
self.sliderPanel.SetSizer(sizer)
# image info
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self.sliderPanel,
box,
title='Image info',
size=wx.DefaultSize)
if sys.platform.startswith(('win', 'linux')):
fsize = 9
else:
fsize = 11
font = wx.Font(fsize, wx.SWISS, wx.NORMAL, wx.NORMAL)
# pixel size
pxsiz = tuple(self.doc.pxlsiz[::-1])
dimstr = ('X', 'Y', 'Z')
line = 'Pixel size (um):\n'
pxstr = ' '
for i, d in enumerate(pxsiz):
if d:
pxstr += '%s %.3f: ' % (dimstr[i], d)
if pxstr:
line += pxstr[:-2]
else:
line = ''
if line:
label = G.makeTxt(self.sliderPanel, box, line)
label.SetFont(font)
# data type
pxtype = imgio.bioformatsIO.pixeltype_to_bioformats(self.doc.dtype)
line = 'Data type: %s' % pxtype
label = G.makeTxt(self.sliderPanel, box, line)
label.SetFont(font)
# z slider
if self.doc.nz > 1:
topSizer = G.newSpaceV(sizer)
#label, self.zSliderBox = G.makeTxtBox(self.sliderPanel, topSizer, 'Z', defValue=str(self.doc.z), tip='enter z idx', style=wx.TE_PROCESS_ENTER)
label, self.zSliderBox = G.makeTxtBox(self.sliderPanel,
topSizer,
'Z',
defValue=self.doc.z,
tip='enter z idx',
style=wx.TE_PROCESS_ENTER)
self.zSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnZSliderBox)
G.makeTxt(self.sliderPanel, topSizer, r'/' + str(self.doc.nz - 1))
self.zSlider = wx.Slider(
self.sliderPanel,
wx.ID_ANY,
self.doc.z,
0,
self.doc.nz - 1,
size=wx.Size(150, -1),
style=wx.SL_HORIZONTAL
| wx.SL_AUTOTICKS) #|wx.SL_LABELS | wx.SL_AUTOTICKS)
topSizer.Add(self.zSlider, 6, wx.ALL | wx.ALIGN_LEFT, 2)
#wx.EVT_SLIDER(self, self.zSlider.GetId(), self.OnZSlider)
self.Bind(wx.EVT_SLIDER, self.OnZSlider, id=self.zSlider.GetId())
#wx.EVT_KEY_DOWN(self, self.zSlider.GetId(), self.OnKeyZSlider)
#self.zSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
if self.doc.nt == 1:
self.sliderPanel.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
self.zSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyZSlider)
#self.Bind(wx.EVT_CHAR, self.OnKeyZSlider)
#/n
box = G.newSpaceV(sizer)
autofocusButton = G.makeButton(self.sliderPanel,
box,
self.OnAutoFocus,
title='Auto focus',
tip='')
#/n
box = G.newSpaceV(sizer)
self.orthogonal_toggle = G.makeToggleButton(
self.sliderPanel,
box,
self.onOrthogonal,
title='Orthogonal projections')
#/n
box = G.newSpaceV(sizer)
self.saveScrButton = G.makeButton(self.sliderPanel,
box,
self.onSaveScr,
title='Save screen')
self.choice_viewers = ['XY', 'XZ', 'ZY']
label, self.viewerch = G.makeListChoice(
self.sliderPanel,
box,
'viewer',
self.choice_viewers,
defValue=[self.choice_viewers[0]])
self.viewerch.Enable(0)
# t slider
if self.doc.nt > 1: ## need a time slider
box = G.newSpaceV(sizer)
label, self.tSliderBox = G.makeTxtBox(self.sliderPanel,
box,
'T',
defValue=str(self.doc.t),
tip='enter time idx',
style=wx.TE_PROCESS_ENTER)
self.tSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnTSliderBox)
G.makeTxt(self.sliderPanel, box, r'/' + str(self.doc.nt - 1))
self.tSlider = wx.Slider(
self.sliderPanel,
wx.ID_ANY,
0,
0,
self.doc.nt - 1,
size=wx.Size(150, -1),
style=wx.SL_HORIZONTAL
| wx.SL_AUTOTICKS) #|wx.SL_LABELS | wx.SL_AUTOTICKS)
box.Add(self.tSlider, 6, wx.ALL | wx.ALIGN_LEFT, 2)
#wx.EVT_SLIDER(self, self.tSlider.GetId(), self.OnTSlider)
self.Bind(wx.EVT_SLIDER, self.OnTSlider, id=self.tSlider.GetId())
if self.doc.nz == 1:
self.sliderPanel.Bind(wx.EVT_KEY_DOWN, self.OnKeyTSlider)
self.tSlider.Bind(wx.EVT_KEY_DOWN, self.OnKeyTSlider)
def __init__(self, parent, fn):
"""
fn: a chromagnon file
"""
wx.Panel.__init__(self, parent, -1)
self.clist = ChromagnonList(self, fn)
self.fn = fn
# start drawing
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, fn)
# \n
box = G.newSpaceV(sizer)
if self.clist.map_str != 'None':
G.makeTxt(self, box, 'Local: ')
self.local_label = G.makeTxt(self, box, self.clist.map_str)
# \n
box = G.newSpaceV(sizer)
self.viewLocalButton = G.makeButton(
self,
box,
self.onViewLocal,
title='View',
tip='View local distortion as a image')
choice = [
str(wave) for wave in self.clist.wave
if wave != self.clist.wave[self.clist.refwave]
]
label, self.wavechoice = G.makeListChoice(self,
box,
'wavelength',
choice,
defValue=choice[0])
self.originalFileButton = G.makeButton(self,
box,
self.onChooseOriginalFile,
title='original image file',
tip='')
default = os.path.splitext(fn)[0]
if default.endswith('chromagnon'):
default = os.path.splitext(default)[0]
if not os.path.isfile(default):
default = ''
label, self.originalFileTxt = G.makeTxtBox(self,
box,
'',
defValue=default,
tip='',
sizeX=200)
choice = [str(factor) for factor in (1, 5, 10, 15, 20)]
label, self.factorchoice = G.makeListChoice(self,
box,
'magnification',
choice,
defValue=choice[2])
self.color_name = ['black'] + [
colstr for colstr in microscope.COLOR_NAME
]
label, self.colorchoice = G.makeListChoice(
self,
box,
'arrow color',
self.color_name,
defValue=self.color_name[-1])
# \n
box = G.newSpaceV(sizer)
G.makeTxt(
self, box,
"The file is a .ome.tif file, and the alignment parameters are stored in it's metadata."
)
else:
# \n
box = G.newSpaceV(sizer)
G.makeTxt(
self, box,
'The file is a text file: rename to ".csv" to open as a spread sheet.'
)
# \n\n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, ' ')
box = G.newSpaceV(sizer)
G.makeTxt(
self, box, 'Pixel size ZYX (um): %.3f %.3f %.3f' %
tuple(self.clist.creader.pxlsiz))
if self.clist.nt > 1:
# \n
box = G.newSpaceV(sizer)
label, self.tSliderBox = G.makeTxtBox(self,
box,
'T',
defValue=str(self.clist.t),
tip='enter time idx',
style=wx.TE_PROCESS_ENTER)
self.tSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnTSliderBox)
G.makeTxt(self, box, r'/' + str(self.clist.nt - 1))
self.tSlider = wx.Slider(self,
wx.ID_ANY,
0,
0,
self.clist.nt - 1,
size=wx.Size(150, -1),
style=wx.SL_HORIZONTAL | wx.SL_AUTOTICKS)
box.Add(self.tSlider, 6, wx.ALL | wx.ALIGN_LEFT, 2)
wx.EVT_SLIDER(self, self.tSlider.GetId(), self.OnTSlider)
# \n
box = G.newSpaceV(sizer)
box.Add(self.clist)
# \n
box = G.newSpaceV(sizer)
self.saveButton = G.makeButton(
self,
box,
self.onExport,
title='Save as...',
tip='Save editted parameter into a chromagnon file'
) #, enable=False)
#self.exportButton = G.makeButton(self, box, self.onExport, title='Export as .csv', tip='Save editted parameter into a comma separated file')
self.clearButton = G.makeButton(self,
box,
self.clearSelected,
title='Remove selected',
tip='Remove one wavelength')
self.addButton = G.makeButton(self,
box,
self.addRow,
title='add wavelength',
tip='Add one wavelength')
self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.clist)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.clist)
def __init__(self, parent, listRef, confdic={}, outdir=None, refwave=None):
self.outdir = None
wx.Dialog.__init__(self, parent, id=-1, title='Extra parameters')
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# -------- output dir -----------
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self, box, title='Output direcotry', size=wx.DefaultSize)
self.outdir_cb = G.makeCheck(self, box, "same as input direcotry", tip='', defChecked=not(bool(outdir)), targetFunc=self.OnOutDirCb)
self.chooseOurDirButton = G.makeButton(self, box, self.OnChooseOutDir, title='Choose', tip='', enable=not(self.outdir_cb.GetValue()))
self.outdir = confdic.get('outdir', '')
self.outdir_label = G.makeTxt(self, box, self.outdir)
self.outdir_label.Enable(not(self.outdir_cb.GetValue()))
# -------- reference wave -----------
if listRef and listRef.columnkeys:
waves1 = [list(listRef.getFile(index)[2].split(',')) for index in listRef.columnkeys]
waves = set()
for wave in waves1:
[waves.add(w) for w in wave]
waves = list(waves)
waves.sort()
if len(waves) > 1:
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self, box, title='Reference wavelength', size=wx.DefaultSize)
if refwave is not None and refwave not in waves:
refwave = None
self.refwave_cb = G.makeCheck(self, box, "auto", tip='', defChecked=not(bool(refwave)), targetFunc=self.OnRefWaveCb)
label, self.refwave_choice = G.makeListChoice(self, box, '', waves, defValue=refwave or waves[0], tip='Reference wavelength that does not move', targetFunc=self.OnRefWaveChoice)
self.refwave_choice.Enable(not(self.refwave_cb.GetValue()))
self.refwave_label = G.makeTxt(self, box, refwave or 'auto')
self.refwave_label.Enable(not(self.refwave_cb.GetValue()))
# -------- z accur -----------
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self, box, title='Z-accuracy', size=wx.DefaultSize)
accurChoice = [str(i) for i in aligner.ACCUR_CHOICE]
label, self.accurListChoice = G.makeListChoice(self, box, 'Iteration of 3D phase correlation', accurChoice, defValue=confdic.get('accur', accurChoice[0]))
# -------- max shift -----------
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self, box, title='Maximum shift the channels are possibly misaligned', size=wx.DefaultSize)
label, self.maxshift_text = G.makeTxtBox(self, box, 'Shift (um)', defValue=confdic.get('max_shift', str(af.MAX_SHIFT)), tip='Maximum shift the channels are possibly misaligned', sizeX=40)
# -------- what to do for time series --------
if listRef and listRef.columnkeys:
nt = max([int(listRef.getFile(index)[3]) for index in listRef.columnkeys])
nw = max([len(listRef.getFile(index)[2].split(',')) for index in listRef.columnkeys])
if nt > 1 and nw > 1:
# \n
box = G.newSpaceV(sizer)
bb, box = G.newStaticBox(self, box, title='Time series with mulitple channels', size=wx.DefaultSize)
choice = ['time', 'channel']
label, self.tseriesListChoice = G.makeListChoice(self, box, 'align', choice, defValue=choice[0], tip='Reference wavelength that does not move', targetFunc=self.OnRefWaveChoice)
# -------- OK and Cancel -----------
btnsizer = wx.StdDialogButtonSizer()
btn = wx.Button(self, wx.ID_OK)
btn.SetDefault()
btnsizer.AddButton(btn)
btn = wx.Button(self, wx.ID_CANCEL)
btnsizer.AddButton(btn)
btnsizer.Realize()
sizer.Add(btnsizer, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 5)
sizer.Fit(self)
def __init__(self, parent, fn):
"""
fn: a chromagnon file
"""
wx.Panel.__init__(self, parent, -1)
self.clist = ChromagnonList(self, fn)
self.fn = fn
# start drawing
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, fn)
# \n
box = G.newSpaceV(sizer)
if self.clist.map_str != 'None':
G.makeTxt(self, box, 'Local: ')
self.local_label = G.makeTxt(self, box, self.clist.map_str)
# \n
box = G.newSpaceV(sizer)
self.viewLocalButton = G.makeButton(self, box, self.onViewLocal, title='View', tip='View local distortion as a image')
choice = [str(wave) for wave in self.clist.wave if wave != self.clist.wave[self.clist.refwave]]
label, self.wavechoice = G.makeListChoice(self, box, 'wavelength', choice, defValue=choice[0])
self.originalFileButton = G.makeButton(self, box, self.onChooseOriginalFile, title='original image file', tip='')
default = os.path.splitext(fn)[0]
if default.endswith('chromagnon'):
default = os.path.splitext(default)[0]
if not os.path.isfile(default):
default = ''
label, self.originalFileTxt = G.makeTxtBox(self, box, '', defValue=default, tip='', sizeX=200)
choice = [str(factor) for factor in (1,5,10,15,20)]
label, self.factorchoice = G.makeListChoice(self, box, 'magnification', choice, defValue=choice[2])
self.color_name = ['black'] + [colstr for colstr in microscope.COLOR_NAME]
label, self.colorchoice = G.makeListChoice(self, box, 'arrow color', self.color_name, defValue=self.color_name[-1])
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, "The file is a tif file, and the alignment parameters are stored in it's metadata.")
else:
# \n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, 'The file is a text file')
# \n\n
box = G.newSpaceV(sizer)
G.makeTxt(self, box, ' ')
box = G.newSpaceV(sizer)
G.makeTxt(self, box, 'Pixel size ZYX (um): %.3f %.3f %.3f' % tuple(self.clist.creader.pxlsiz))
if self.clist.nt > 1:
# \n
box = G.newSpaceV(sizer)
label, self.tSliderBox = G.makeTxtBox(self, box, 'T', defValue=str(self.clist.t), tip='enter time idx', style=wx.TE_PROCESS_ENTER)
self.tSliderBox.Bind(wx.EVT_TEXT_ENTER, self.OnTSliderBox)
G.makeTxt(self, box, r'/'+str(self.clist.nt-1))
self.tSlider = wx.Slider(self, wx.ID_ANY, 0, 0,
self.clist.nt-1,
size=wx.Size(150,-1),
style = wx.SL_HORIZONTAL | wx.SL_AUTOTICKS)
box.Add(self.tSlider, 6, wx.ALL|wx.ALIGN_LEFT, 2)
wx.EVT_SLIDER(self, self.tSlider.GetId(), self.OnTSlider)
# \n
box = G.newSpaceV(sizer)
box.Add(self.clist)
# \n
box = G.newSpaceV(sizer)
self.saveButton = G.makeButton(self, box, self.onExport, title='Save as...', tip='Save editted parameter into a chromagnon file')#, enable=False)
#self.exportButton = G.makeButton(self, box, self.onExport, title='Export as .csv', tip='Save editted parameter into a comma separated file')
self.clearButton = G.makeButton(self, box, self.clearSelected, title='Remove selected', tip='Remove one wavelength')
self.addButton = G.makeButton(self, box, self.addRow, title='add wavelength', tip='Add one wavelength')
self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.clist)
self.Bind(wx.EVT_LIST_ITEM_DESELECTED, self.OnItemSelected, self.clist)