def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
numpy.save(outFile, data[xslice, yslice, zslice])
if not metadata is None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName is None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
#xmd.WriteSimple(xmlFile)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
#nframes = (zslice.stop - zslice.start)/zslice.step
outDir = os.path.splitext(outFile)[0]
os.mkdir(outDir)
i = 0
for frameN in range(zslice.start, zslice.stop, zslice.step):
im = data[xslice, yslice, frameN].squeeze()[None, :, :]
for fN in range(frameN + 1, frameN + zslice.step):
im += data[xslice, yslice, fN].squeeze()[None, :, :]
Image.fromarray(im.squeeze().astype('uint16'), 'I;16').save(
os.path.join(outDir, 'frame_%03d.tif' % i))
i += 1
if not metadata is None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName is None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
# xmd.WriteSimple(xmlFile)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
def _findAndParseMetadata(self, filename):
"""Try and find and load a .xml or .md metadata file that might be ascociated
with a given image filename. See the relevant metadatahandler classes
for details."""
import xml.parsers.expat
from PYME.IO import unifiedIO
if not self.mdh is None:
return #we already have metadata (probably passed in on command line)
mdf = None
xmlfn = os.path.splitext(filename)[0] + '.xml'
xmlfnmc = os.path.splitext(filename)[0].split('__')[0] + '.xml'
if os.path.exists(xmlfn):
try:
self.mdh = MetaDataHandler.NestedClassMDHandler(
MetaData.TIRFDefault)
self.mdh.copyEntriesFrom(MetaDataHandler.XMLMDHandler(xmlfn))
mdf = xmlfn
except xml.parsers.expat.ExpatError:
#fix for bug in which PYME .md was written with a .xml extension
self.mdh = MetaDataHandler.NestedClassMDHandler(
MetaData.BareBones)
self.mdh.copyEntriesFrom(
MetaDataHandler.SimpleMDHandler(xmlfn))
mdf = xmlfn
elif os.path.exists(
xmlfnmc): #this is a single colour channel of a pair
self.mdh = MetaDataHandler.NestedClassMDHandler(
MetaData.TIRFDefault)
self.mdh.copyEntriesFrom(MetaDataHandler.XMLMDHandler(xmlfnmc))
mdf = xmlfnmc
else:
self.mdh = MetaDataHandler.NestedClassMDHandler(MetaData.BareBones)
#check for simple metadata (python code with an .md extension which
#fills a dictionary called md)
mdfn = os.path.splitext(filename)[0] + '.md'
jsonfn = os.path.splitext(filename)[0] + '.json'
if os.path.exists(mdfn):
self.mdh.copyEntriesFrom(MetaDataHandler.SimpleMDHandler(mdfn))
mdf = mdfn
elif os.path.exists(jsonfn):
import json
with open(jsonfn, 'r') as f:
mdd = json.load(f)
self.mdh.update(mdd)
elif filename.endswith('.lsm'):
#read lsm metadata
from PYME.contrib.gohlke.tifffile import TIFFfile
tf = TIFFfile(filename)
lsm_info = tf[0].cz_lsm_scan_information
self.mdh['voxelsize.x'] = lsm_info['line_spacing']
self.mdh['voxelsize.y'] = lsm_info['line_spacing']
self.mdh['voxelsize.z'] = lsm_info['plane_spacing']
def lsm_pop(basename, dic):
for k, v in dic.items():
if isinstance(v, list):
#print k, v
for i, l_i in enumerate(v):
#print i, l_i, basename
lsm_pop(
basename + k + '.' + k[:-1] + '%i.' % i,
l_i)
else:
self.mdh[basename + k] = v
lsm_pop('LSM.', lsm_info)
elif filename.endswith('.tif'):
#look for OME data...
from PYME.contrib.gohlke.tifffile import TIFFfile
tf = TIFFfile(filename)
if tf.is_ome:
try:
omemdh = MetaDataHandler.OMEXMLMDHandler(
tf.pages[0].tags['image_description'].value)
self.mdh.copyEntriesFrom(omemdh)
except IndexError:
pass
elif filename.endswith('.dcimg'): #Bewersdorf lab Biplane
# FIXME load seriesXX.json for seriesXX_chunkXX.dcimg files more elegantly
jsonfn = filename[:-22] + '.json'
import json
try:
mdd = json.loads(unifiedIO.read(jsonfn))
self.mdh.update(mdd)
except IOError:
pass
elif filename.endswith('.dbl'): #Bewersdorf lab STED
mdfn = filename[:-4] + '.txt'
entrydict = {}
try: #try to read in extra metadata if possible
with unifiedIO.openFile(mdfn, 'r') as mf:
for line in mf:
s = line.split(':')
if len(s) == 2:
entrydict[s[0]] = s[1]
except IOError:
pass
# vx, vy = entrydict['Pixel size (um)'].split('x')
# self.mdh['voxelsize.x'] = float(vx)
# self.mdh['voxelsize.y'] = float(vy)
# self.mdh['voxelsize.z'] = 0.2 #FIXME for stacks ...
#
# sx, sy = entrydict['Image format'].split('x')
# self.mdh['Camera.ROIWidth'] = int(sx)
# self.mdh['Camera.ROIHeight'] = int(sy)
#
# self.mdh['NumImages'] = int(entrydict['# Images'])
with unifiedIO.openFile(filename) as df:
s = df.read(8)
Z, X, Y, T = numpy.fromstring(s, '>u2')
s = df.read(16)
depth, width, height, elapsed = numpy.fromstring(s, '<f4')
self.mdh['voxelsize.x'] = width / X
self.mdh['voxelsize.y'] = height / Y
self.mdh['voxelsize.z'] = depth
self.mdh['Camera.ROIWidth'] = X
self.mdh['Camera.ROIHeight'] = Y
self.mdh['NumImages'] = Z * T
def _sanitise_key(key):
k = key.replace('#', 'Num')
k = k.replace('(%)', '')
k = k.replace('(', '')
k = k.replace(')', '')
k = k.replace('.', '')
k = k.replace('/', '')
k = k.replace('?', '')
k = k.replace(' ', '')
if not k[0].isalpha():
k = 's' + k
return k
for k, v in entrydict.items():
self.mdh['STED.%s' % _sanitise_key(k)] = v
#else: #try bioformats
# OMEXML = bioformats.get_omexml_metadata(filename).encode('utf8')
# OMEmd = MetaDataHandler.OMEXMLMDHandler(OMEXML)
# self.mdh.copyEntriesFrom(OMEmd)
if self.haveGUI and not ('voxelsize.x' in self.mdh.keys()
and 'voxelsize.y' in self.mdh.keys()):
from PYME.DSView.voxSizeDialog import VoxSizeDialog
dlg = VoxSizeDialog(None)
dlg.ShowModal()
self.mdh.setEntry('voxelsize.x', dlg.GetVoxX())
self.mdh.setEntry('voxelsize.y', dlg.GetVoxY())
self.mdh.setEntry('voxelsize.z', dlg.GetVoxZ())
return mdf
def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
#numpy.save(outFile, data[xslice, yslice, zslice])
#import cPickle
try:
chanNames = metadata.getEntry('ChannelNames')
except:
chanNames = ['Chan %d' % d for d in range(data.shape[4])]
dat = [
data[xslice, yslice, zslice, :, chan].squeeze()
for chan in range(data.shape[4])
]
#print chanNames
if metadata and 'Profile.XValues' in metadata.getEntryNames():
dat = [metadata.getEntry('Profile.XValues')] + dat
chanNames = [metadata.getEntry('Profile.XLabel')] + chanNames
if metadata and 'Spectrum.Wavelengths' in metadata.getEntryNames():
dat = [metadata.getEntry('Spectrum.Wavelengths')] + dat
chanNames = ['Wavelength [nm]'] + chanNames
fid = open(outFile, 'wb')
#write header
fid.write(('#' + '\t'.join(chanNames)).encode('utf-8'))
for i in range(len(dat[0])):
fid.write(
('\n' + '\t'.join(['%f' % d[i] for d in dat])).encode('utf-8'))
fid.close()
# write metadata in xml file
if not metadata is None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName is None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
warnings.warn(
'export of old style tiffs should only be used in exceptional circumstances'
)
#xmd = None
if not metadata is None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if data.shape[3] > 1: #have multiple colour channels
if data.shape[2] == 1: #2d image -> stack with chans
#d = numpy.concatenate([numpy.atleast_3d(data[xslice, yslice, 0, i].squeeze()) for i in range(data.shape[3])],2)
#saveTiffStack.saveTiffMultipage(d, outFile)
mpt = saveTiffStack.TiffMP(outFile)
for i in range(data.shape[3]):
mpt.AddSlice(data[xslice, yslice, 0, i].squeeze())
mpt.close()
else: #save each channel as it's own stack
if not metadata is None and 'ChannelNames' in metadata.getEntryNames(
):
chanNames = metadata['ChannelNames']
else:
chanNames = range(data.shape[3])
chanFiles = [
os.path.splitext(os.path.split(outFile)[1])[0] +
'__%s.tif' % chanNames[i] for i in range(data.shape[3])
]
if not metadata is None:
xmd['ChannelFiles'] = chanFiles
for i in range(data.shape[3]):
saveTiffStack.saveTiffMultipage(
data[xslice, yslice, zslice, i].squeeze(),
os.path.splitext(outFile)[0] +
'__%s.tif' % chanNames[i])
else:
saveTiffStack.saveTiffMultipage(data[xslice, yslice, zslice],
outFile)
if not metadata is None:
#xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName is None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
print((xslice.indices(data.shape[0])))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
# xmd.WriteSimple(xmlFile)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
