def _load_func(self, fn):
if chromformat.is_chromagnon(fn):
h = chromformat.ChromagnonReader(fn)
else:
try:
h = imgio.Reader(fn)
except ValueError as e:
return listbox.imgio_dialog(e, self)
if aligner.hasSameWave(h):
dlg = wx.MessageDialog(
self,
'The image contains multiple channels with the same wavelength. Please use a unique wavelength for each channel',
'Error in channel wavelengths',
wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
if h.nseries > 1:
dlg = wx.MessageDialog(
self,
'Multiple series data sets are not allowed, please make a file with a single image in a file',
'Error in image file', wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
self.lastpath = os.path.dirname(fn)
C.saveConfig(lastpath=self.lastpath)
return h
def __init__(self,
parent,
imFile=None,
id=wx.ID_ANY,
pos=wx.DefaultPosition,
size=wx.DefaultSize):
wx.Panel.__init__(self, parent, id, pos, size, name='')
# to make consistent with the older viewers
self.parent = self
self._mgr = aui.AuiManager()
self._mgr.SetManagedWindow(self)
self._perspectives = []
## self.doc contains all the information on the displayed image
if isinstance(imFile, six.string_types): #str):
self.doc = imgio.Reader(
imFile) #bioformatsIO.load(imFile)#aligner.Chromagnon(imFile)
else:
self.doc = imFile
#self.zsec = [self.doc.nz//2]
#self.zlast = [0]
if self.doc:
self.doc.zlast = 0
self.addImageXY()
def makeFlatConv(fn, out=None, suffix=''):
"""
save a calibration file
return output file name
"""
if not out:
out = os.path.splitext(fn)[0] + suffix + os.path.extsep + EXT
elif not out.endswith(EXT):
out = os.path.extsep.join(os.path.splitext(out)[0], EXT)
h = imgio.Reader(fn) #bioformatsIO.load(fn)
ntz = h.nz * h.nt
o = imgio.Writer(fn) #bioformatsIO.getWriter(out)
o.setFromReader(h)
o.nt = 1
o.nz = 1
o.dtype = N.float32
o.ome.add_structured_annotation('idtype', IDTYPE)
for w in range(h.nw):
canvas = N.zeros((h.nt, h.nz, h.ny, h.nx), N.float32)
for t in range(h.nt):
for z in range(h.nz):
canvas[t, z] = h.getArr(w=w, t=t, z=z)
arr = canvas.reshape((ntz, h.ny, h.nx)).mean(axis=0)
arr = arr.mean() / arr
o.writeArr(arr.astype(N.float32), w=w, z=0)
o.close()
h.close()
return out
def flatConv(fn, flatFile, out=None, suffix='_' + EXT.upper()):
"""
save a normalized image
return output filename
"""
if not out:
base, ext = os.path.splitext(fn)
out = base + suffix + ext
h = imgio.Reader(fn) #bioformatsIO.load(fn)
f = imgio.Reader(flatFile) #bioformatsIO.load(flatFile)
o = imgio.Writer(out) #bioformatsIO.getWriter(out)
o.setFromReader(h)
if out.endswith('ome.tif'):
o.imgSequence = 0
for w in range(h.nw):
tgt_wave = h.getWaveFromIdx(w)
if tgt_wave in f.wave:
rw = h.getWaveIdx(tgt_wave)
fs = f.getArr(w=rw, z=0)
for t in range(h.nt):
for z in range(h.nz):
a = h.getArr(w=w, t=t, z=z)
b = a * fs
o.writeArr(b.astype(h.dtype), w=w, t=t, z=z)
else:
for t in range(h.nt):
for z in range(h.nz):
a = h.getArr(w=w, t=t, z=z)
o.writeArr(a.astype(h.dtype), w=w, t=t, z=z)
o.close()
h.close()
f.close()
return out
def is_flat(fn, check_img_to_open=True):
check = False
if fn.endswith(EXT):
check = True
else:
if check_img_to_open:
rdr = imgio.Reader(fn) #bioformatsIO.BioformatsReader(fn)
if hasattr(rdr, 'ome') and \
rdr.ome.get_structured_annotation('idtype') == IDTYPE:
check = True
rdr.close()
return check
def _load_func(self, fn):
try:
h = imgio.Reader(fn) #bioformatsIO.load(fn)
except ValueError:
dlg = wx.MessageDialog(self, '%s is not a valid image file!' % ff,
'Error reading image file',
wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
if h.nseries > 1:
dlg = wx.MessageDialog(
self,
'Multiple series data sets are not allowed, please make a file with a single image in a file',
'Error in image file', wx.OK | wx.ICON_EXCLAMATION)
if dlg.ShowModal() == wx.ID_OK:
return
return h
default=aligner.WRITABLE_FORMATS[0],
choices=aligner.WRITABLE_FORMATS,
help=
'file extension for the target files, choose from %s (default=%s)'
% (aligner.WRITABLE_FORMATS, aligner.WRITABLE_FORMATS[0]))
options = p.parse_args()
ref = glob.glob(
os.path.expandvars(os.path.expanduser(options.reference)))
fns = []
for fn in options.targets:
fns += glob.glob(os.path.expandvars(os.path.expanduser(fn)))
nts = []
for fn in fns:
h = imgio.Reader(fn) #bioformatsIO.load(fn)
nts.append(h.nt)
h.close()
parms = [
True, # crop mergins
None, #options.initguess,
options.local,
options.maxShift,
options.zmag,
options.parm_suffix,
options.img_suffix,
nts,
options.img_format,
int(options.localMinWindow)
]
def __init__(self, fn):
"""
usage:
## channel alignment
## fn: the reference image
>>> an = Chromagnon(fn)
>>> an.findBestChannel()
>>> an.findAlignParamWave()
>>> an.setRegionCutOut()
>>> an.saveAlignedImage()
>>> out = an.saveParm()
## fn2: the target image
>>> an = Chromagnon(fn2)
>>> an.loadParm(out)
>>> an.setRegionCutOut()
>>> out = an.saveAlignedImage()
## time frame alignment
## fn: the reference image (time projected for 10 frames for example)
>>> an = Chromagnon(fn)
>>> an.findBestTimeFrame()
>>> an.findAlignParamTime()
>>> an.setRegionCutOut()
>>> an.saveAlignedImage()
"""
self.img = imgio.Reader(fn)
self.copyAttr()
self.setMaxError()
self.setMaxIter()
self.setReferenceTime()
self.setReferenceWave()
self.setReferenceZIndex()
self.setReferenceXIndex()
self.setImageCenter()
self.setMultipageTiff()
self.setphaseContrast()
self.setEchofunc()
self.setProgressfunc()
self.setImgSuffix()
self.setFileFormats()
self.setParmSuffix()
self.setIf_failed()
self.alignParms = N.zeros((self.img.nt, self.img.nw, NUM_ENTRY), N.float32)
self.alignParms[:,:,4:] = 1
self.cropSlice = [Ellipsis, slice(None), slice(None), slice(None)]
self.saturation = N.zeros((self.img.nt, self.img.nw, 3))
self.refyz = None
self.refyx = None
self.mapyx = None
self.regions = None
self.byteorder = '<'
self.setCCthreshold()
self.setMaxShift()
self.setZmagSwitch()
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 main(fn, out=None, otf=None, **kwds):
# setup
priismCommands.PriismSetup()
# byteSwap for Softworx
if 'littleEndian' in kwds:
littleEndian = kwds.pop('littleEndian')
else:
littleEndian = False
#bilateral
if 'filterMethod' in kwds:
filterMethod = kwds.pop('filterMethod')
else:
filterMethod = None
makelog = kwds.pop('makelog', None)
if filterMethod:
OPTS = [opt for opt in DECON_OPT] # copy
if not filterMethod.startswith('f'):
OPTS += FFT_OPT
fkwds = dict([(key, val) for key, val in kwds.items()
if key not in OPTS])
fn = priismCommands.Filter3D(fn,
out,
filterMethod=filterMethod,
**fkwds)
if littleEndian:
out = os.path.extsep.join((fn, byteSwap.DEF_EXT))
#byteSwap.byteSwap(fn, out)
# replacing byteSwap
h = imgio.Reader(fn) #mrcIO.MrcReader(fn)
o = imgio.Writer(
out, hdr=h.hdr,
byteorder='<') #mrcIO.MrcWriter(out, h.hdr, byteorder='<')
for t in range(h.nt):
for w in range(h.w):
o.write3DArr(h.get3DArr(t=t, w=w), t=t, w=w)
o.close()
h.close()
os.remove(fn)
fn = out
# decon filename
if not out or filterMethod:
out = fn + EXT_DCN
log = os.path.extsep.join((out, 'log'))
# decon otf
if isinstance(otf, six.string_types) and os.path.exists(otf):
ctf = otf
elif isinstance(otf, six.string_types) and otf.isdigit():
ctf = findOTFfromNum(otf)
else:
ctf = findOTF(fn)
# decon
options = []
for key, value in kwds.items():
if key in DECON_OPT:
if value == True:
options.append('-%s' % key)
else:
options.append('-%s=%s' % (key, value))
#title = 'OTFfile:%s' % shortenStr(ctf)
#com = ' '.join(['decon %s %s %s -title="%s" ' % (fn, out, ctf, title)] + options)
com = ' '.join(['decon %s %s %s ' % (fn, out, ctf)] + options)
if PRINTOUT:
print(com)
if makelog:
if os.path.exists(log):
os.remove(log)
com += ' >> %s' % log
h = open(log, 'a')
h.write(com)
if sys.platform == 'darwin':
out2 = saveCommand(com)
import subprocess
err = subprocess.call(['sh', out2])
os.remove(out2)
else:
err = os.system(com)
if err:
raise RuntimeError(
'Deconvolution failed (exit status %s)\ncommand is: %s' %
(err, com))
if makelog:
h.close()
if littleEndian:
fn = out
out = os.path.extsep.join((fn, byteSwap.DEF_EXT))
#byteSwap.byteSwap(fn, out)
h = imgio.Reader(fn) #mrcIO.MrcReader(fn)
o = imgio.Writer(
out, hdr=h.hdr,
byteorder='<') #mrcIO.MrcWriter(out, h.hdr, byteorder='<')
#h = mrcIO.MrcReader(fn)
#o = mrcIO.MrcWriter(out, h.hdr, byteorder='<')
for t in range(h.nt):
for w in range(h.w):
o.write3DArr(h.get3DArr(t=t, w=w), t=t, w=w)
o.close()
h.close()
os.remove(fn)
if PRINTOUT:
print('Done %s' % out)
return out
