def __init__(self, filename='', metadata=None, taskQueue=None):
if filename is not '':
self.filename = getFullExistingFilename(
filename) #convert relative path to full path
#use metadata for glob
md = MetaDataHandler.SimpleMDHandler(self.filename)
else:
md = metadata
self.filename = ''
pattern = md.getEntry('SeriesPattern')
self.files = glob.glob(
os.path.join(os.path.split(self.filename)[0], pattern))
self.files.sort()
f0 = self.files[0]
if f0.endswith('.tif'):
self.im0 = tifffile.imread(f0).squeeze()
self._slice_shape = self.im0.shape[:2]
else:
self.im0 = Image.open(self.files[0])
self._slice_shape = self.im0.size[1], self.im0.size[0]
#self.im.seek(0)
#PIL's endedness support is subtly broken - try to fix it
#NB this is untested for floating point tiffs
self.endedness = 'LE'
if self.im0.ifd.prefix == 'MM':
self.endedness = 'BE'
print((self.im0.ifd.prefix))
print((self.endedness))
def __init__(self, filename, taskQueue=None):
self.filename = getFullExistingFilename(
filename) #convert relative path to full path
#self.data = readTiff.read3DTiff(self.filename)
#use metadata for glob
md = MetaDataHandler.SimpleMDHandler(self.filename)
pattern = md.getEntry('SeriesPattern')
self.files = glob.glob(
os.path.join(os.path.split(self.filename)[0], pattern))
self.files.sort()
self.im0 = Image.open(self.files[0])
#self.im.seek(0)
#PIL's endedness support is subtly broken - try to fix it
#NB this is untested for floating point tiffs
self.endedness = 'LE'
if self.im0.ifd.prefix == 'MM':
self.endedness = 'BE'
print((self.im0.ifd.prefix))
print((self.endedness))
def fromMDFile(cls, mdfile):
"""
Create a new fit test jig from a metadata file
Parameters
----------
mdfile - string
the filename of the metadata file to use. The file should be in PYMEs 'SimpleMDHandler' (*.md) format.
Returns
-------
fitTestJig instance
"""
return cls(MetaDataHandler.SimpleMDHandler(mdfile))
def fromMDFile(cls, mdfile):
return cls(MetaDataHandler.SimpleMDHandler(mdfile))
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
