def restoreState(self, state, rootPath=None):
if state.get('contents', None) != 'MosaicEditor_save':
raise TypeError("This does not appear to be MosaicEditor save data.")
if state['version'][0] > self._saveVersion[0]:
raise TypeError("Save data has version %d.%d, but this MosaicEditor only supports up to version %d.x." % (state['version'][0], state['version'][1], self._saveVersion[0]))
if not self.clear():
return
root = state['rootPath']
if root == '':
# data was stored with no root path; filenames should be absolute
root = None
else:
# data was stored with no root path; filenames should be relative to the loaded file
root = DataManager.getHandle(rootPath)
for itemState in state['items']:
fname = itemState['filename']
if root is None:
fh = DataManager.getHandle(fh)
else:
fh = root[fname]
item = self.addFile(fh, name=itemState['name'], inheritTransform=False)
item.restoreState(itemState)
self.canvas.view.setState(state['view'])
def getSiteNWBs(basepath):
""" Get all experiment NWBs in the slice*/site* folders """
matches = []
dirHandleBase = adm.getHandle(basepath)
dirHandleBase.checkIndex()
# start in basepath
for k in dirHandleBase.ls():
if not dirHandleBase.isManaged(k):
continue
slicePath = os.path.join(basepath, k)
if os.path.isfile(slicePath):
continue
# base/slice
dirHandleSlice = adm.getHandle(slicePath)
dirHandleSlice.checkIndex()
for k in dirHandleSlice.ls():
if not dirHandleSlice.isManaged(k):
continue
sitePath = os.path.join(slicePath, k)
if os.path.isfile(sitePath):
continue
# base/slice/site
all_nwbs = glob.glob(os.path.join(sitePath, '*.nwb'))
all_pxps = glob.glob(os.path.join(sitePath, '*.pxp'))
if len(all_nwbs) != 1:
print "The site folder \"%s\" will be ignored as it holds more than one NWB file." % sitePath
print all_nwbs
continue
if len(all_pxps) != 1:
print "The site folder \"%s\" will be ignored as it holds more than one PXP file." % sitePath
print all_pxps
continue
siteNWB = all_nwbs[0]
sitePXP = all_pxps[0]
if not os.path.isfile(siteNWB):
print "The site folder \"%s\" will be ignored as it is missing the mandatory NWB file." % sitePath
continue
if not os.path.isfile(sitePXP):
print "The site folder \"%s\" will be ignored as it is missing the mandatory PXP file." % sitePath
continue
matches.append(os.path.abspath(siteNWB))
return matches
def restoreState(self, state, rootPath=None):
if state.get('contents', None) != 'MosaicEditor_save':
raise TypeError(
"This does not appear to be MosaicEditor save data.")
if state['version'][0] > self._saveVersion[0]:
raise TypeError(
"Save data has version %d.%d, but this MosaicEditor only supports up to version %d.x."
% (state['version'][0], state['version'][1],
self._saveVersion[0]))
if not self.clear():
return
root = state['rootPath']
if root == '':
# data was stored with no root path; filenames should be absolute
root = None
else:
# data was stored with no root path; filenames should be relative to the loaded file
root = DataManager.getHandle(rootPath)
loadfail = []
for itemState in state['items']:
fname = itemState.get('filename')
if fname is None:
# create item from scratch and restore state
itemtype = itemState.get('type')
if itemtype not in items.itemTypes():
# warn the user later on that we could not load this item
loadfail.append((itemState.get('name'),
'Unknown item type "%s"' % itemtype))
continue
item = self.addItem(type=itemtype, name=itemState['name'])
else:
# normalize file name for this OS
revsep = {'/': '\\', '\\': '/'}[os.path.sep]
fname = fname.replace(revsep, os.path.sep)
# create item by loading file and restore state
if root is None:
fh = DataManager.getHandle(fh)
else:
fh = root[fname]
item = self.addFile(fh,
name=itemState['name'],
inheritTransform=False)
item.restoreState(itemState)
self.canvas.view.setState(state['view'])
if len(loadfail) > 0:
msg = "\n".join(["%s: %s" % m for m in loadfail])
raise Exception("Failed to load some items:\n%s" % msg)
def getSiteNWBs(basepath):
""" Get all experiment NWBs in the slice*/site* folders """
matches = []
dirHandleBase = adm.getHandle(basepath)
dirHandleBase.checkIndex()
# start in basepath
for k in dirHandleBase.ls():
if not dirHandleBase.isManaged(k):
continue
slicePath = os.path.join(basepath, k)
if os.path.isfile(slicePath):
continue
# base/slice
dirHandleSlice = adm.getHandle(slicePath)
dirHandleSlice.checkIndex()
for k in dirHandleSlice.ls():
if not dirHandleSlice.isManaged(k):
continue
sitePath = os.path.join(slicePath, k)
if os.path.isfile(sitePath):
continue
# base/slice/site
all_nwbs = glob.glob(os.path.join(sitePath, '*.nwb'))
if len(all_nwbs) != 1:
print "The site folder \"%s\" will be ignored as it holds not exactly one NWB file." % sitePath
print all_nwbs
continue
siteNWB = all_nwbs[0]
if not os.path.isfile(siteNWB):
print "The site folder \"%s\" will be ignored as it is missing the mandatory NWB file." % sitePath
continue
matches.append(os.path.abspath(siteNWB))
return matches
def addSiteContents(siteNWBs, filesToInclude, slicePath, siteName):
""" Add site specific entries to the NWB file """
sitePath = os.path.join(slicePath, siteName)
siteIndex = os.path.join(sitePath, ".index")
if len(siteNWBs) != 1:
print "Expected exactly one NWB file belonging to site folder %s, skipping it." % sitePath
return 1
sitePXP = glob.glob(os.path.join(sitePath, '*.pxp'))[0]
addDataSource(siteNWBs, sitePXP)
dh = adm.getHandle(sitePath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, "%s_index_meta" % siteName, data)
appendMiscFileToNWB(siteNWBs, "%s_index" % siteName,
getFileContents(siteIndex))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.join(sitePath, k)
if os.path.isdir(path):
raise NameError("Unexpected folder \"%s\" in \"%s\"." %
(k, sitePath))
elif os.path.isfile(path): # check if we need to handle it
if fileShouldBeSkipped(path, filesToInclude):
continue
filedesc = encodeAsJSONString(dh[k].info())
if path.endswith(".tif"):
appendImageFileToNWB(siteNWBs, path, filedesc)
elif path.endswith(".ma"):
appendMAFile(siteNWBs, path, filedesc)
elif path.endswith(".log"):
appendPseudoYamlLog(siteNWBs, path, k, filedesc)
else:
raise NameError(
"Unexpected file type \"%s\" in index \"%s\"." %
(k, siteIndex))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"." %
(k, siteIndex))
def __init__(self, atlas, host):
Atlas.AtlasCtrlWidget.__init__(self, atlas, host)
self.atlasDir = os.path.split(os.path.abspath(__file__))[0]
## add ThalamocorticalMarker to canvas
fh = DataManager.getHandle(os.path.join(self.atlasDir, 'images', 'ThalamocorticalMarker.svg'))
self.canvas.addFile(fh, pos=(-0.001283, -0.000205), scale=[3.78e-6, 3.78e-6], index=0, movable=False, z=10000)
## add CortexROI
self.roi = CortexROI([-1e-3, 0])
self.canvas.addGraphicsItem(self.roi, pos=(-1e-3, 1e-3), scale=[1e-3, 1e-3], name='CortexROI', movable=False)
self.roi.sigRegionChangeFinished.connect(self.roiChanged)
def buildCombinedNWBInternal(basepath, siteNWBs, filesToInclude):
""" NOT FOR PUBLIC USE """
# we have three types of keys in the main index file
# ---------------------------------------------------------------------
# '.' | common description of the experiment | (unique)
# '$existingFile' | log file of the experiment | (multiple)
# '$existingFolder' | different slices for each experiment | (multiple)
dh = adm.getHandle(basepath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, basename="main_index_meta", content=data)
logfile = os.path.join(basepath, '.index')
appendMiscFileToNWB(siteNWBs,
basename="main_index",
content=getFileContents(logfile))
for elem in siteNWBs:
os.remove(deriveOutputNWB(elem))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.abspath(os.path.join(basepath, k))
if os.path.isdir(path): # slice folder
addSliceContents(siteNWBs, filesToInclude, basepath, k)
elif os.path.isfile(path): # main log file
data = encodeAsJSONString(dh[k].info())
appendMiscFileToNWB(siteNWBs,
basename="main_logfile_meta",
content=data)
appendMiscFileToNWB(siteNWBs,
basename="main_logfile",
content=getFileContents(path))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"" %
(k, logfile))
combinedNWBs = []
for elem in siteNWBs:
combinedNWBs.append(deriveOutputNWB(elem))
return combinedNWBs
def addSliceContents(siteNWBs, filesToInclude, basepath, sliceName):
""" Add entries to the slice specific NWB file """
slicePath = os.path.join(basepath, sliceName)
sliceIndex = os.path.join(slicePath, ".index")
sliceNWBs = [elem for elem in siteNWBs if elem.startswith(slicePath)]
if len(sliceNWBs) == 0:
#print "No NWB files belong to slice folder %s, skipping it." % slicePath
return 1
dh = adm.getHandle(slicePath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, "%s_index_meta" % sliceName, data)
appendMiscFileToNWB(siteNWBs, "%s_index" % sliceName,
getFileContents(sliceIndex))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.abspath(os.path.join(slicePath, k))
filedesc = encodeAsJSONString(dh[k].info())
if os.path.isdir(path): # site folder
appendMiscFileToNWB(sliceNWBs, "%s_%s" % (sliceName, k), filedesc)
addSiteContents(sliceNWBs, filesToInclude, slicePath, k)
elif os.path.isfile(path): # check if we need to handle it
if fileShouldBeSkipped(path, filesToInclude):
continue
if path.endswith(".tif"):
appendImageFileToNWB(sliceNWBs, path, filedesc)
elif path.endswith(".ma"):
appendMAFile(sliceNWBs, path, filedesc)
else:
raise NameError("Unexpected file type \"%s\" in index \"%s\"" %
(k, sliceIndex))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"" %
(k, sliceIndex))
def addSiteContents(siteNWBs, filesToInclude, slicePath, siteName):
""" Add site specific entries to the NWB file """
sitePath = os.path.join(slicePath, siteName)
siteIndex = os.path.join(sitePath, ".index")
if len(siteNWBs) != 1:
print "Expected exactly one NWB file belonging to site folder %s, skipping it." % sitePath
return 1
addDataSource(siteNWBs)
dh = adm.getHandle(sitePath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, "%s_index_meta" % siteName, data)
appendMiscFileToNWB(siteNWBs, "%s_index" % siteName, getFileContents(siteIndex))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.join(sitePath, k)
if os.path.isdir(path):
raise NameError("Unexpected folder \"%s\" in \"%s\"." % (k, sitePath))
elif os.path.isfile(path): # check if we need to handle it
if fileShouldBeSkipped(path, filesToInclude):
continue
filedesc = encodeAsJSONString(dh[k].info())
if path.endswith(".tif"):
appendImageFileToNWB(siteNWBs, path, filedesc)
elif path.endswith(".ma"):
appendMAFile(siteNWBs, path, filedesc)
elif path.endswith(".log"):
appendPseudoYamlLog(siteNWBs, path, k, filedesc)
else:
raise NameError("Unexpected file type \"%s\" in index \"%s\"." % (k, siteIndex))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"." % (k, siteIndex))
def uiChanged(self):
for item in self.images:
self.canvas.removeItem(item)
self.images = []
state = self.stateGroup.state()
slice = state['slicePlaneCombo']
hem = state['hemisphereCombo']
#flip = state['flipCheck']
imgs = self.slicePlanes[slice]
atlasDir = os.path.split(os.path.abspath(__file__))[0]
for imgFile, scale, pos in imgs:
fh = DataManager.getHandle(os.path.join(atlasDir, 'images', imgFile))
item = self.canvas.addFile(fh, pos=pos, scale=[scale,scale], index=0, movable=False, z=10000)
#item = self.canvas.addFile(fh, index=0, movable=False)
self.images.append(item)
def buildCombinedNWBInternal(basepath, siteNWBs, filesToInclude):
""" NOT FOR PUBLIC USE """
# we have three types of keys in the main index file
# ---------------------------------------------------------------------
# '.' | common description of the experiment | (unique)
# '$existingFile' | log file of the experiment | (multiple)
# '$existingFolder' | different slices for each experiment | (multiple)
dh = adm.getHandle(basepath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, basename = "main_index_meta", content = data)
logfile = os.path.join(basepath, '.index')
appendMiscFileToNWB(siteNWBs, basename = "main_index", content = getFileContents(logfile))
for elem in siteNWBs:
os.remove(deriveOutputNWB(elem))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.abspath(os.path.join(basepath, k))
if os.path.isdir(path): # slice folder
addSliceContents(siteNWBs, filesToInclude, basepath, k)
elif os.path.isfile(path): # main log file
data = encodeAsJSONString(dh[k].info())
appendMiscFileToNWB(siteNWBs, basename = "main_logfile_meta", content = data)
appendMiscFileToNWB(siteNWBs, basename = "main_logfile", content = getFileContents(path))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"" % (k, logfile))
combinedNWBs = []
for elem in siteNWBs:
combinedNWBs.append(deriveOutputNWB(elem))
return combinedNWBs
def addSliceContents(siteNWBs, filesToInclude, basepath, sliceName):
""" Add entries to the slice specific NWB file """
slicePath = os.path.join(basepath, sliceName)
sliceIndex = os.path.join(slicePath, ".index")
sliceNWBs = [elem for elem in siteNWBs if elem.startswith(slicePath)]
if len(sliceNWBs) == 0:
#print "No NWB files belong to slice folder %s, skipping it." % slicePath
return 1
dh = adm.getHandle(slicePath)
dh.checkIndex()
data = encodeAsJSONString(dh["."].info())
appendMiscFileToNWB(siteNWBs, "%s_index_meta" % sliceName, data)
appendMiscFileToNWB(siteNWBs, "%s_index" % sliceName, getFileContents(sliceIndex))
for k in dh.ls():
if not dh.isManaged(k):
continue
path = os.path.abspath(os.path.join(slicePath, k))
filedesc = encodeAsJSONString(dh[k].info())
if os.path.isdir(path): # site folder
appendMiscFileToNWB(sliceNWBs, "%s_%s" % (sliceName, k), filedesc)
addSiteContents(sliceNWBs, filesToInclude, slicePath, k)
elif os.path.isfile(path): # check if we need to handle it
if fileShouldBeSkipped(path, filesToInclude):
continue
if path.endswith(".tif"):
appendImageFileToNWB(sliceNWBs, path, filedesc)
elif path.endswith(".ma"):
appendMAFile(sliceNWBs, path, filedesc)
else:
raise NameError("Unexpected file type \"%s\" in index \"%s\"" % (k, sliceIndex))
else:
raise NameError("Unexpected key \"%s\" in index \"%s\"" % (k, sliceIndex))
def baseDir(self):
"""Return a dirHandle for the base directory used for all file names in the database."""
if self._baseDir is None:
dirName = self.ctrlParam('BaseDirectory')
self._baseDir = DataManager.getHandle(dirName)
return self._baseDir
def baseDir(self):
"""Return a dirHandle for the base directory used for all file names in the database."""
if self._baseDir is None:
dirName = self.ctrlParam('BaseDirectory')
self._baseDir = DataManager.getHandle(dirName)
return self._baseDir
