def addRow(self, evt=None):
"""
add a row to the list and self.clist.alignParms
"""
if self.clist.nw >= 5:
G.openMsg(self, 'The maximum wavelength is 5',
'I am sorry for that')
return
if wx.version().startswith('3'):
index = self.InsertStringItem(sys.maxsize, '0')
else:
index = self.clist.InsertItem(sys.maxsize, '0')
self.clist.alignParms = N.insert(self.clist.alignParms,
self.clist.alignParms.shape[1],
0,
axis=1)
self.clist.alignParms[:, -1, -3:] = 1
waves = list(self.clist.waves)
waves.append(0)
self.clist.waves = N.array(waves)
self.clist.nw = len(self.clist.waves)
for i, p in enumerate(self.clist.alignParms[self.clist.t, index]):
self.clist.SetItem(index, i + 1,
str(p)) #SetStringItem(index, i+1, str(p))
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 OnAutoFocus(self, evt=None):
"""
please read Chromagnon.alignfuncs.findBestRefZs() for detail of the logic
"""
if self.doc.nt > 1:
t = int(self.tSliderBox.GetValue())
else:
t = 0
ws = [
w for w, hist in enumerate(self.hist_toggleButton)
if hist.GetValue()
]
ms = N.zeros((len(ws), self.doc.nz), N.float32)
# FFTW does not work with another program using it
# here is the workaround for Chromagnon
try:
batch = self.GetParent().GetParent().GetParent()
if hasattr(batch, 'th') and batch.th.isAlive():
for wi, w in enumerate(ws):
arr = self.doc.get3DArr(t=t, w=w)
for z in range(self.doc.nz):
ms[wi, z] = N.prod(U.mmms(arr[z])[-2:]) # mean * std
v, _, w, z = U.findMax(ms)
self.zSliderBox.SetValue(str(z))
self.OnZSliderBox()
self.OnAutoScale()
G.openMsg(
parent=self.parent,
msg=
'A clumsy focusing method was used since another program was using FFTW.\nPlease wait for the better method until the other program is done.',
title="Please wait")
return
except AttributeError: # no parent?
pass
# Frequency-based caluculation starts
from Priithon.all import F
ring = F.ringArr(self.doc.shape[-2:],
radius1=self.doc.shape[-1] // 10,
radius2=self.doc.shape[-2] // 4,
orig=(0, 0),
wrap=1)
for wi, w in enumerate(ws):
arr = self.doc.get3DArr(t=t, w=w)
arr = arr / arr.mean()
for z in range(self.doc.nz):
af = F.rfft(N.ascontiguousarray(arr[z]))
ar = af * ring[:, :af.shape[-1]]
ms[wi, z] = N.sum(N.abs(ar))
v, _, w, z = U.findMax(ms)
self.zSliderBox.SetValue(str(z))
self.OnZSliderBox()
self.OnAutoScale()
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 OnAutoFocus(self, evt=None):
"""
please read Chromagnon.alignfuncs.findBestRefZs() for detail of the logic
"""
if self.doc.nt > 1:
t = int(self.tSliderBox.GetValue())
else:
t = 0
ws = [w for w, hist in enumerate(self.hist_toggleButton) if hist.GetValue()]
ms = N.zeros((len(ws),self.doc.nz), N.float32)
# FFTW does not work with another program using it
# here is the workaround for Chromagnon
try:
batch = self.GetParent().GetParent().GetParent()
if hasattr(batch, 'th') and batch.th.isAlive():
for wi, w in enumerate(ws):
arr = self.doc.get3DArr(t=t, w=w)
for z in range(self.doc.nz):
ms[wi,z] = N.prod(U.mmms(arr[z])[-2:]) # mean * std
v,_,w,z = U.findMax(ms)
self.zSliderBox.SetValue(str(z))
self.OnZSliderBox()
self.OnAutoScale()
G.openMsg(parent=self.parent, msg='A clumsy focusing method was used since another program was using FFTW.\nPlease wait for the better method until the other program is done.', title="Please wait")
return
except AttributeError: # no parent?
pass
# Frequency-based caluculation starts
from Priithon.all import F
ring = F.ringArr(self.doc.shape[-2:], radius1=self.doc.shape[-1]//10, radius2=self.doc.shape[-2]//4, orig=(0,0), wrap=1)
for wi, w in enumerate(ws):
arr = self.doc.get3DArr(t=t, w=w)
arr = arr / arr.mean()
for z in range(self.doc.nz):
af = F.rfft(N.ascontiguousarray(arr[z]))
ar = af * ring[:,:af.shape[-1]]
ms[wi,z] = N.sum(N.abs(ar))
v,_,w,z = U.findMax(ms)
self.zSliderBox.SetValue(str(z))
self.OnZSliderBox()
self.OnAutoScale()
def view(self, fn):
"""
opens viewer and hide itself.
"""
try:
self.doc = aligner.Chromagnon(fn)
except:
G.openMsg(self, 'This file is not a valid image file', 'Error')
return
self.loadParm()
parent = self.GetParent()
parent._mgr.GetPane('tpanel').Hide()
parent.addImageXY()
def view(self, fn):
"""
opens viewer and hide itself.
"""
try:
self.doc = aligner.Chromagnon(fn)
self.doc.zlast = 0
except:
G.openMsg(self, 'This file is not a valid image file', 'Error')
return
self.loadParm()
parent = self.GetParent()
parent._mgr.GetPane('tpanel').Hide()
parent.addImageXY()
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 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 addRow(self, evt=None):
"""
add a row to the list and self.clist.alignParms
"""
if self.clist.nw >= 5:
G.openMsg(self, 'The maximum wavelength is 5', 'I am sorry for that')
return
if wx.version().startswith('3'):
index = self.InsertStringItem(sys.maxsize, '0')
else:
index = self.clist.InsertItem(sys.maxsize, '0')
self.clist.alignParms = N.insert(self.clist.alignParms, self.clist.alignParms.shape[1], 0, axis=1)
self.clist.alignParms[:,-1,-3:] = 1
waves = list(self.clist.waves)
waves.append(0)
self.clist.waves = N.array(waves)
self.clist.nw = len(self.clist.waves)
for i, p in enumerate(self.clist.alignParms[self.clist.t,index]):
self.clist.SetItem(index, i+1, str(p))#SetStringItem(index, i+1, str(p))
def onViewLocal(self, evnt=None, gridStep=60, t=0, w=None, originalFn=None, **kwds):
"""
save a '.local' file and opens new image viewer
"""
import wx, tempfile
import imgio
from Priithon.all import Y
if w is None:
wave = int(self.wavechoice.GetStringSelection())
w = self.clist.wave.index(wave)
if originalFn is None:
originalFn = self.originalFileTxt.GetValue()
factor = int(self.factorchoice.GetStringSelection())
colstr = self.colorchoice.GetStringSelection()
colortable = [(0,0,0)] + microscope.COLOR_TABLE
col = colortable[self.color_name.index(colstr)]
parent = self.GetParent()
book = parent.GetTopLevelParent()
mapyx = self.clist.mapyx
name = self.clist.basename + '.Local'
if originalFn:
try:
img = imgio.Reader(originalFn)#imgfileIO.load(originalFn)
except:
G.openMsg(self, 'Is this file really a image file?', title='Error')
return
if N.any(N.array(img.shape[-2:]) != N.array(self.clist.mapyx.shape[-2:])):
G.openMsg(self, 'Please choose original image file BEFORE alignment', title='Error')
return
a = N.zeros(self.clist.mapyx.shape[-3:], img.dtype)
b = img.get3DArr(w=self.clist.refwave, t=t)
if self.clist.mapyx.ndim == 5:
b = N.max(b, 0)
a[0] = b
b = img.get3DArr(w=w, t=t)
if self.clist.mapyx.ndim == 5:
b = N.max(b, 0)
a[1] = af.applyShift(b, self.clist.alignParms[t,w])
pz, py, px = img.pxlsiz
else:
a = N.zeros(self.clist.mapyx.shape[-3:], N.uint8)
pz = py = px = 1
out = os.path.join(tempfile.gettempdir(), 'Chromagnon.local.tif')
wtr = imgio.Writer(out)
wtr.setPixelSize(pz=pz, py=py, px=px)
wtr.setDim(nx=a.shape[-1], ny=a.shape[-2], nz=1, nt=1, nw=2, dtype=a.dtype.type, wave=[self.clist.wave[self.clist.refwave], self.clist.wave[w]], imgSequence=1)
for w, a2d in enumerate(a):
wtr.writeArr(a2d, w=w)
wtr.close()
an = aligner.Chromagnon(out)
newpanel = aui.ImagePanel(book, an.img)
book.imEditWindows.AddPage(newpanel, name, select=True)
v = newpanel.viewers[0]
wx.Yield()
inds = N.indices(mapyx.shape[-2:], N.float32)
slcs1 = [slice(gridStep//2, -gridStep//2, gridStep) for d in range(2)]
#for w in xrange(self.clist.nw):
vs = []
for d in range(2):
slcs = [slice(d,d+1)] + slcs1
vs.append(inds[slcs].ravel())
iis = N.array(list(zip(*vs)))
vs = []
for d in range(2):
slcs = [slice(t,t+1), slice(w,w+1), slice(d,d+1)] + slcs1
vs.append(mapyx[slcs].ravel())
yxs = N.array(list(zip(*vs)))
wave = self.clist.wave[w]
#col = microscope.LUT(wave)
#col = (1,1,1)
wx.CallAfter(Y.vgAddArrows, v, iis, iis+yxs, color=col, factor=factor, width=2, **kwds)
def quit(self, message='', title='ERROR'):
if message:
G.openMsg(parent=self, msg=message, title=title)
self.goButton.SetValue(0)
self.label.SetLabel('')
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 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 ChromagnonReader(fn, rdr=None, holder=None):
rdr = rdr
holder = holder
dratio = N.ones((3, ), N.float32)
if not is_binary(fn):
text = True
fp = open(fn)
reader = csv.reader(fp)
# read parameters
nt = int(reader.next()[1])
nw = int(reader.next()[1])
pxlsiz = N.array([eval(p) for p in reader.next()[1:]])
imgSequence = 2
refwave = eval(reader.next()[1])
num_entry = len(reader.next()[2:])
wave = []
#self.pos0 = self.tell()
alignParms = N.empty((nt, nw, num_entry), N.float32)
for t in xrange(nt):
for w in xrange(nw):
row = reader.next()
wave.append(_eval(row[1]))
alignParms[t, w] = [eval(v) for v in row[2:]]
else:
text = False
reader = bioformatsIO.BioformatsReader(fn)
pxlsiz = reader.pxlsiz
wave = reader.wave
nw = reader.nw
nt = reader.nt
nz = reader.nz
nz //= 2
ny = reader.ny
nx = reader.nx
# read parameters
refwave = eval(reader.ome.get_structured_annotation('refwave'))
num_entry = eval(reader.ome.get_structured_annotation('num_entry'))
alignParms = N.empty((reader.nt, reader.nw, reader.num_entry),
N.float32)
for t in xrange(reader.nt):
for w in xrange(reader.nw):
for i, key in enumerate(DIMSTRS):
alignParms[t, w, i] = eval(
reader.ome.get_structured_annotation('t%03d_w%i_' %
(t, w) + key))
# loading parameters to the parent classes
if rdr and holder:
# reading the header
if hasattr(rdr, 'pxlsiz'):
dratio = N.asarray(pxlsiz, N.float32) / N.asarray(
rdr.pxlsiz, N.float32)
else: # chromeditor
dratio = N.ones((3, ), N.float32)
rdr.pxlsiz = pxlsiz
rdr.wave = wave
rdr.nw = nw
rdr.nt = nt
rdr.nz = nz
# wavelength difference
pwaves = list(wave[:nw])
twaves = list(rdr.wave[:rdr.nw])
tids = [twaves.index(wave) for wave in pwaves if wave in twaves]
pids = [pwaves.index(wave) for wave in twaves if wave in pwaves]
somewaves = [w for w, wave in enumerate(pwaves) if wave in twaves]
if refwave in twaves:
holder.refwave = twaves.index(refwave)
elif len(
somewaves
) >= 1: # the reference wavelength was not found but some found
holder.refwave = somewaves[0]
from PriCommon import guiFuncs as G
message = 'The original reference wavelength %i of the initial guess was not found in the target %s' % (
refwave, holder.file)
G.openMsg(msg=message, title='WARNING')
else:
from PriCommon import guiFuncs as G
message = 'No common wavelength with initial guess was found in %s and %s' % (
os.path.basename(file), rdr.file)
G.openMsg(msg=message, title='WARNING')
return
# compensate wavelength difference
target = N.zeros((nt, rdr.nw, num_entry), N.float32)
target[:, :, 4:] = 1
target[:, tids] = alignParms[:, pids]
for w in [w for w, wave in enumerate(twaves) if wave not in pwaves]:
target[:, w] = alignParms[:, holder.refwave]
target[:, :, :3] *= dratio
alignParms = target
# set holder
if hasattr(self.holder, 'setAlignParam'):
holder.setAlignParam(alignParms)
else:
holder.alignParms = alignParms
# obtain mapping array
if not text:
nzyx = N.array((nz, reader.ny, reader.nx), N.float32)
nzyx *= dratio
nyzx = nzyx.astype(N.int)
tmin = min(rdr.nt, reader.nt)
if nzyx[0] > 1:
arr = N.zeros((rdr.nt, rdr.nw, nzyx[0], 2, nzyx[1], nzyx[2]),
reader.dtype)
else:
arr = N.zeros((rdr.nt, rdr.nw, 2, nzyx[1], nzyx[2]),
reader.dtype)
for t in xrange(tmin):
for wt, wp in enumerate(pids):
w = tids[wt]
a = N.zeros((nzyx[0], 2, nzyx[1], nzyx[2]), reader.dtype)
for z in xrange(nz):
warr = reader.get3DArr(t=t, w=w)
warr = warr.reshape((nz, 2, reader.ny, reader.nx))
for s in xrange(2):
zc = z * 2 + s
if any(dratio[1:] != 1):
a[z, s] = nd.zoom(warr[:, s],
dratio) * dratio[1 + (s % 2)]
else:
arr[z, s] = warr[:, s]
if nzyx[0] > 1:
arr[t, w] = a
else:
arr[t, w] = a[0]
for w in [
w for w, wave in enumerate(twaves) if wave not in pwaves
]:
arr[:tmin, w] = arr[:tmin, refwave]
holder.mapyx = arr
return reader
def onViewLocal(self,
evnt=None,
gridStep=60,
t=0,
w=None,
originalFn=None,
**kwds):
"""
save a '.local' file and opens new image viewer
"""
import wx, tempfile
import imgio
from Priithon.all import Y
if w is None:
wave = int(self.wavechoice.GetStringSelection())
w = self.clist.wave.index(wave)
if originalFn is None:
originalFn = self.originalFileTxt.GetValue()
factor = int(self.factorchoice.GetStringSelection())
colstr = self.colorchoice.GetStringSelection()
colortable = [(0, 0, 0)] + microscope.COLOR_TABLE
col = colortable[self.color_name.index(colstr)]
parent = self.GetParent()
book = parent.GetTopLevelParent()
mapyx = self.clist.mapyx
name = self.clist.basename + '.Local'
if originalFn:
try:
img = imgio.Reader(originalFn) #imgfileIO.load(originalFn)
except:
G.openMsg(self,
'Is this file really a image file?',
title='Error')
return
if N.any(
N.array(img.shape[-2:]) != N.array(
self.clist.mapyx.shape[-2:])):
G.openMsg(self,
'Please choose original image file BEFORE alignment',
title='Error')
return
a = N.zeros(self.clist.mapyx.shape[-3:], img.dtype)
b = img.get3DArr(w=self.clist.refwave, t=t)
if self.clist.mapyx.ndim == 5:
b = N.max(b, 0)
a[0] = b
b = img.get3DArr(w=w, t=t)
if self.clist.mapyx.ndim == 5:
b = N.max(b, 0)
a[1] = af.applyShift(b, self.clist.alignParms[t, w])
pz, py, px = img.pxlsiz
else:
a = N.zeros(self.clist.mapyx.shape[-3:], N.uint8)
pz = py = px = 1
out = os.path.join(tempfile.gettempdir(), 'Chromagnon.local.tif')
wtr = imgio.Writer(out)
wtr.setPixelSize(pz=pz, py=py, px=px)
wtr.setDim(
nx=a.shape[-1],
ny=a.shape[-2],
nz=1,
nt=1,
nw=2,
dtype=a.dtype.type,
wave=[self.clist.wave[self.clist.refwave], self.clist.wave[w]],
imgSequence=1)
for w, a2d in enumerate(a):
wtr.writeArr(a2d, w=w)
wtr.close()
an = aligner.Chromagnon(out)
newpanel = aui.ImagePanel(book, an.img)
book.imEditWindows.AddPage(newpanel, name, select=True)
v = newpanel.viewers[0]
wx.Yield()
inds = N.indices(mapyx.shape[-2:], N.float32)
slcs1 = [
slice(gridStep // 2, -gridStep // 2, gridStep) for d in range(2)
]
#for w in xrange(self.clist.nw):
vs = []
for d in range(2):
slcs = [slice(d, d + 1)] + slcs1
vs.append(inds[slcs].ravel())
iis = N.array(list(zip(*vs)))
vs = []
for d in range(2):
slcs = [slice(t, t + 1), slice(w, w + 1), slice(d, d + 1)] + slcs1
vs.append(mapyx[slcs].ravel())
yxs = N.array(list(zip(*vs)))
wave = self.clist.wave[w]
#col = microscope.LUT(wave)
#col = (1,1,1)
wx.CallAfter(Y.vgAddArrows,
v,
iis,
iis + yxs,
color=col,
factor=factor,
width=2,
**kwds)
def loadParm(self):
"""
load a chromagnon file
"""
# reading the header
if hasattr(self.rdr, 'pxlsiz'):
self.dratio = N.asarray(self.pxlsiz, N.float32) / N.asarray(
self.rdr.pxlsiz, N.float32)
else: # chromeditor
self.dratio = N.ones((3, ), N.float32)
self.rdr.pxlsiz = self.pxlsiz
self.rdr.wave = self.wave
self.rdr.nw = self.nw
self.rdr.nt = self.nt
self.rdr.nz = self.nz
# wavelength difference
self.pwaves = [int(round(w)) for w in self.wave[:self.nw]]
self.twaves = [int(round(w)) for w in self.rdr.wave[:self.rdr.nw]]
self.tids = [
self.twaves.index(wave) for wave in self.pwaves
if wave in self.twaves
]
self.pids = [
self.pwaves.index(wave) for wave in self.twaves
if wave in self.pwaves
]
somewaves = [
w for w, wave in enumerate(self.pwaves) if wave in self.twaves
]
if self.refwave in self.twaves:
self.holder.refwave = self.twaves.index(self.refwave)
elif len(
somewaves
) >= 1: # the reference wavelength was not found but some found
self.holder.refwave = somewaves[0]
from PriCommon import guiFuncs as G
message = 'The original reference wavelength %i of the initial guess was not found in the target %s' % (
self.refwave, self.holder.fn)
G.openMsg(msg=message, title='WARNING')
else:
#self.holder.parm = N.zeros((self.rdr.nt, self.rdr.nw, self.num_entry), self.dtype)
from PriCommon import guiFuncs as G
message = 'No common wavelength with initial guess was found in %s and %s' % (
os.path.basename(self.file), self.rdr.file)
G.openMsg(msg=message, title='WARNING')
return
# obtain affine parms
self.readParmWave()
if hasattr(self.holder, 'setAlignParam'):
self.holder.setAlignParam(self.alignParms)
else:
self.holder.alignParms = self.alignParms
# obtain mapping array
if not self.text:
self.holder.mapyx = self.readMapAll()