def saveStack(self, event=None):
fdialog = wx.FileDialog(
None,
'Save Data Stack as ...',
defaultDir=self.filedir,
wildcard='KDF (*.kdf)|*.kdf|TIFF (*.tif)|*.tif',
style=wx.FD_SAVE | wx.HIDE_READONLY)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
fpath = fdialog.GetPath()
if os.path.splitext(fpath)[1] == '.kdf':
self.ds.SaveToFile(fdialog.GetPath())
else:
#save using PIL
if self.ds.getNumChannels() == 1:
#im = Image.fromarray(cSMI.CDataStack_AsArray(self.ds, 0), 'I;16')
#im.save(fpath)
im = cSMI.CDataStack_AsArray(self.ds, 0).squeeze()
saveTiffStack.writeTiff(im, fpath)
else:
fst, ext = os.path.splitext(fpath)
for i in range(self.ds.getNumChannels()):
#im = Image.fromarray(cSMI.CDataStack_AsArray(self.ds, i), 'I;16')
#im.save(fst + '_%d'%i + ext)
im = cSMI.CDataStack_AsArray(self.ds, i).squeeze()
saveTiffStack.writeTiff(im, fst + '_%d' % i + ext)
if not (self.log is None):
lw = logparser.logwriter()
s = lw.write(self.log)
log_f = open('%s.log' % fdialog.GetPath().split('.')[0], 'w')
log_f.write(s)
log_f.close()
self.SetTitle(fdialog.GetFilename())
self.saved = True
def generateThumbnail(inputFile, thumbSize):
global size
im = cSMI.CDataStack_AsArray(cSMI.CDataStack(inputFile.encode()),
0).mean(2).squeeze()
xsize = im.shape[0]
ysize = im.shape[1]
if xsize > ysize:
zoom = float(thumbSize) / xsize
else:
zoom = float(thumbSize) / ysize
size = (int(xsize * zoom), int(ysize * zoom))
im = im - im.min()
im = maximum(minimum(1 * (255 * im) / im.max(), 255), 0)
return im.astype('uint8')
def LoadKdf(self, filename):
'''load khorus formatted data - pretty much deprecated by now'''
import PYME.cSMI as cSMI
self.data = cSMI.CDataStack_AsArray(cSMI.CDataStack(filename),
0).squeeze()
self.mdh = MetaData.TIRFDefault
try: #try and get metadata from the .log file
lf = open(os.path.splitext(filename)[0] + '.log')
from PYME.DSView import logparser
lp = logparser.logparser()
log = lp.parse(lf.read())
lf.close()
self.mdh.setEntry('voxelsize.z', log['PIEZOS']['Stepsize'])
except:
pass
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
def calcSum(caller):
Is.append(cSMI.CDataStack_AsArray(caller.ds, 0).sum())