def __init__(self, **kwargs):
EMObject.__init__(self, **kwargs)
self.grid = String()
self.gridSquare = String()
self.hole = String()
self.x = Float()
self.y = Float()
def updateItemMaxCC(self, item, row):
from convert import locationToXmipp
# ToDo: uncomment this lines when the output metadata has ITEM_ID
# if item.getObjId() != row.getValue(xmipp.MDL_ITEM_ID):
# raise Exception("The objId is not equal to ITEM_ID. Please, sort the metadata.")
if isinstance(item, Class2D):
img = item.getRepresentative()
index, fn = img.getLocation()
else:
index, fn = item.getLocation()
# objLoc = locationToXmipp(index, fn)
# mdLoc = row.getValue(md.MDL_IMAGE)
# if objLoc != mdLoc:
# raise Exception("The image isn't the same. Please, sort the metadata.")
if item.getObjId() != row.getValue(md.MDL_ITEM_ID):
raise Exception(
"The image isn't the same. Please, sort the metadata.")
item._xmipp_imageRef = String(row.getValue(md.MDL_IMAGE_REF))
item._xmipp_image = String(row.getValue(md.MDL_IMAGE))
item._xmipp_imageResidual = String(row.getValue(md.MDL_IMAGE_RESIDUAL))
item._xmipp_maxCC = Float(row.getValue(md.MDL_MAXCC))
item._xmipp_cost = Float(row.getValue(md.MDL_COST))
if isinstance(item, Class2D):
particle = item.getRepresentative()
else:
particle = item
def _setPsdFiles(self, ctfModel, micDir):
ctfModel._psdFile = String(self._getFileName('psd', micDir=micDir))
ctfModel._xmipp_enhanced_psd = \
String(self._getFileName('enhanced_psd', micDir=micDir))
ctfModel._xmipp_ctfmodel_quadrant = \
String(self._getFileName('ctfmodel_quadrant', micDir=micDir))
ctfModel._xmipp_ctfmodel_halfplane = \
String(self._getFileName('ctfmodel_halfplane', micDir=micDir))
def __init__(self, **kwargs):
OrderedObject.__init__(self, **kwargs)
self.label = String(kwargs.get('label', None))
self.hostName = String(kwargs.get('hostName', None))
self.userName = String()
self.password = String()
self.hostPath = String()
self.mpiCommand = String()
self.scipionHome = String()
self.scipionConfig = String()
self.address = String()
self.queueSystem = QueueSystemConfig()
def _loadInputCoords(self, micDict):
""" Load coordinates from the input streaming.
"""
coordsFn = self.getCoords().getFileName()
self.debug("Loading input db: %s" % coordsFn)
coordSet = SetOfCoordinates(filename=coordsFn)
# FIXME: Temporary to avoid loadAllPropertiesFail
coordSet._xmippMd = String()
coordSet.loadAllProperties()
for micKey, mic in micDict.iteritems():
micId = mic.getObjId()
coordList = []
self.debug("Loading coords for mic: %s (%s)" % (micId, micKey))
for coord in coordSet.iterItems(where='_micId=%s' % micId):
# TODO: Check performance penalty of using this clone
coordList.append(coord.clone())
self.debug(" Coords found: %s" % len(coordList))
if coordList:
self.coordDict[micId] = coordList
else:
del micDict[micKey]
self.coordsClosed = coordSet.isStreamClosed()
coordSet.close()
self.debug("Coords are closed? %s" % self.coordsClosed)
self.debug("Closed db.")
return micDict
def readSetOfCoordinates(outputDir, partSet, coordSet):
"""This method is used to store an edition of the coordinates obtained by
localized reconstruction.
Read from Xmipp .pos files.
Params:
outputDir: the directory where the .pos files are.
It is also expected a file named: config.xmd
in this directory where the box size can be read.
micSet: the SetOfMicrographs to associate the .pos, which
name should be the same of the micrographs.
coordSet: the SetOfCoordinates that will be populated.
"""
# Read the boxSize from the config.xmd metadata
configfile = join(outputDir, 'config.xmd')
if exists(configfile):
mdFn = md.MetaData('properties@' + join(outputDir, 'config.xmd'))
boxSize = mdFn.getValue(md.MDL_PICKING_PARTICLE_SIZE,
mdFn.firstObject())
coordSet.setBoxSize(boxSize)
for part in partSet:
baseFn = "%06d_at_%s" % (part.getIndex(),
replaceBaseExt(part.getFileName(), 'pos'))
posFile = join(outputDir, baseFn)
readCoordinates(part, posFile, coordSet, outputDir)
coordSet._xmippMd = String(outputDir)
def createChimeraScript(self, volume, pdb):
""" Create a chimera script to visualize a pseudoatoms pdb
obteined from a given EM 3d volume.
A property will be set in the pdb object to
store the location of the script.
"""
pseudoatoms = pdb.getFileName()
scriptFile = pseudoatoms + '_chimera.cmd'
pdb._chimeraScript = String(scriptFile)
sampling = volume.getSamplingRate()
radius = sampling * self.pseudoAtomRadius.get()
fnIn = volume.getFileName()
localInputFn = self._getBasePath(fnIn)
createLink(fnIn, localInputFn)
fhCmd = open(scriptFile, 'w')
fhCmd.write("open %s\n" % basename(pseudoatoms))
fhCmd.write("rangecol bfactor,a 0 white 1 red\n")
fhCmd.write("setattr a radius %f\n" % radius)
fhCmd.write("represent sphere\n")
fhCmd.write("open %s\n" % basename(localInputFn))
threshold = 0.01
if self.maskMode == NMA_MASK_THRE:
self.maskThreshold.get()
xdim = volume.getDim()[0]
origin = xdim / 2
fhCmd.write(
"volume #1 level %f transparency 0.5 voxelSize %f originIndex %d\n"
% (threshold, sampling, origin))
fhCmd.close()
def _methods(self):
methods = []
if not hasattr(self, 'outputVolumes'):
methods.append("Output volumes not ready yet.")
else:
inputIsString = ''
if isinstance(self.inputParticles.get(), SetOfParticles):
methods.append(
'Set of %d particles %s was employed to create an initial volume using RCT method.'
% (len(self.inputParticles.get()),
self.getObjectTag('inputParticles')))
else:
particlesArray = [len(s) for s in self.inputParticles.get()]
particlesArrayString = String(particlesArray)
methods.append(
'Set of %d classes %s was employed to create %d initial volumes using RCT method. '
% (len(self.inputParticles.get()),
self.getObjectTag('inputParticles'),
len(self.inputParticles.get())))
methods.append(
'For each initial volume were used respectively %s particles'
% particlesArrayString)
methods.append("Output volumes: %s" %
self.getObjectTag('outputVolumes'))
if self.doFilter.get():
methods.append("Output filtered volumes: %s" %
self.getObjectTag('outputFilteredVolumes'))
return methods
def createOutputStep(self):
outputVols = self._createSetOfVolumes()
imgSet = self.inputParticles.get()
for i, vol in enumerate(self._iterInputVols()):
volume = vol.clone()
volDir = self._getVolDir(i + 1)
volPrefix = 'vol%03d_' % (i + 1)
validationMd = self._getExtraPath(volPrefix + 'validation.xmd')
moveFile(join(volDir, 'validation.xmd'), validationMd)
clusterMd = self._getExtraPath(volPrefix +
'clusteringTendency.xmd')
moveFile(join(volDir, 'clusteringTendency.xmd'), clusterMd)
outImgSet = self._createSetOfParticles(volPrefix)
outImgSet.copyInfo(imgSet)
outImgSet.copyItems(imgSet,
updateItemCallback=self._setWeight,
itemDataIterator=md.iterRows(
clusterMd, sortByLabel=md.MDL_ITEM_ID))
mdValidatoin = md.MetaData(validationMd)
weight = mdValidatoin.getValue(md.MDL_WEIGHT,
mdValidatoin.firstObject())
volume.weight = Float(weight)
volume.clusterMd = String(clusterMd)
volume.cleanObjId(
) # clean objects id to assign new ones inside the set
outputVols.append(volume)
self._defineOutputs(outputParticles=outImgSet)
outputVols.setSamplingRate(volume.getSamplingRate())
self._defineOutputs(outputVolumes=outputVols)
def __init__(self, **kwargs):
OrderedObject.__init__(self, **kwargs)
self.name = String('default')
self.maxCores = Integer()
self.allowMPI = Boolean()
self.allowThreads = Boolean()
self.maxHours = Integer()
def _checkNewInput(self):
newMics = []
for idx, coordSet in enumerate(self.inputCoordinates):
coorSet = SetOfCoordinates(filename=coordSet.get().getFileName())
coorSet._xmippMd = String()
coorSet.loadAllProperties()
self.streamClosed = coorSet.isStreamClosed()
coorSet.close()
if self.check[idx] == "":
newMics.append(
[c.clone() for c in coordSet.get().getMicrographs()])
else:
newMics.append([
c.clone()
for c in coordSet.get().getMicrographs().iterItems(
orderBy='creation',
where='creation>"' + str(self.check[idx]) + '"')
])
if len(newMics[idx]) < 1:
continue
else:
for p in coordSet.get().getMicrographs().iterItems(
orderBy='creation', direction='DESC'):
self.check[idx] = p.getObjCreation()
break
newMics[:] = [item for item in newMics if len(item) > 0]
if len(newMics) > 0:
fDeps = self.insertNewCoorsSteps(min(newMics, key=len))
self.inputMics = self.inputMics + len(min(newMics, key=len))
outputStep = self._getFirstJoinStep()
if outputStep is not None:
outputStep.addPrerequisites(*fDeps)
self.updateSteps()
def _updateParticle(self, item, row):
item.setClassId(row.getValue(md.MDL_REF))
item.setTransform(rowToAlignment(row, ALIGN_2D))
if self.flag_relion:
item._rlnLogLikeliContribution = Float(None)
item._rlnMaxValueProbDistribution = Float(None)
item._rlnGroupName = String(None)
item._rlnNormCorrection = Float(None)
def _updateItem(self, particle, row):
self.reader.setParticleTransform(particle, row)
# FIXME: check if other attrs need saving
particle._rlnImageOriginalName = String(row.rlnImageOriginalName)
particle._rlnRandomSubset = Integer(row.rlnRandomSubset)
newLoc = convert.relionToLocation(row.rlnImageName)
particle.setLocation(newLoc)
def setPsdFiles(ctfModel, ctfRow):
""" Set the PSD files of CTF estimation related
to this ctfModel. The values will be read from
the ctfRow if present.
"""
for attr, label in CTF_PSD_DICT.iteritems():
if ctfRow.containsLabel(label):
setattr(ctfModel, attr, String(ctfRow.getValue(label)))
def getReadyMics(coordSet):
coorSet = SetOfCoordinates(filename=coordSet.getFileName())
coorSet._xmippMd = String()
coorSet.loadAllProperties()
setClosed = coorSet.isStreamClosed()
coorSet.close()
currentPickMics = {
micAgg["_micId"]
for micAgg in coordSet.aggregate(["MAX"], "_micId", ["_micId"])
}
return currentPickMics, setClosed
def _defineProcessParams(self, form):
# First we customize the inputParticles param to fit our needs in this protocol
form.getParam('inputParticles').pointerCondition = String('hasAlignment')
form.getParam('inputParticles').help = String('Input images you want to filter. It is important that the images have alignment information with '
'respect to the chosen set of classes. This is the standard situation '
'after CL2D or ML2D.')
form.addParam('inputClasses', PointerParam, label='Input Classes', important=True,
pointerClass='SetOfClasses',
help='Select the input classes for the basis construction against images will be projected to.')
form.addSection(label='Basis construction')
form.addParam('maxClasses', IntParam, default=128,
label='Max. number of classes', expertLevel=LEVEL_ADVANCED,
help='Maximum number of classes.')
form.addParam('maxPCABases', IntParam, default=200,
label='Number of PCA bases', expertLevel=LEVEL_ADVANCED,
help='Number of PCA bases.')
form.addSection(label='Denoising')
form.addParam('PCABases2Project', IntParam, default=200,
label='Number of PCA bases on which to project', expertLevel=LEVEL_ADVANCED,
help='Number of PCA bases on which to project.')
def _loadInputCoords(self, micDict):
""" Load coordinates from the input streaming.
"""
# TODO: this takes for ever if you are NOT
# doing streaming and have several thousands of mics
# so I add a counter to keep the user entertained
import sys
a = datetime.now()
counter = 1
coordsFn = self.getCoords().getFileName()
self.debug("Loading input db: %s" % coordsFn)
coordSet = SetOfCoordinates(filename=coordsFn)
# FIXME: Temporary to avoid loadAllPropertiesFail
coordSet._xmippMd = String()
coordSet.loadAllProperties()
# TODO: horrible code. Rewrite using
# for coord in coordSet.iterItems(orderBy='_micId',
# direction='ASC'):
# micId = coord.getMicId()
# if micId != lastMicId:
# lastMicId = micId
# ...
# ...
for micKey, mic in micDict.iteritems():
if counter % 50 == 0:
b = datetime.now()
print(b - a, 'reading coordinates for mic number',
"%06d" % counter)
sys.stdout.flush() # force buffer to print
counter += 1
micId = mic.getObjId()
coordList = []
self.debug("Loading coords for mic: %s (%s)" % (micId, micKey))
for coord in coordSet.iterItems(where='_micId=%s' % micId):
# TODO: Check performance penalty of using this clone
coordList.append(coord.clone())
self.debug("Coords found: %s" % len(coordList))
if coordList:
self.coordDict[micId] = coordList
else:
del micDict[micKey]
self.coordsClosed = coordSet.isStreamClosed()
coordSet.close()
self.debug("Coords are closed? %s" % self.coordsClosed)
self.debug("Closed db.")
return micDict
def writeSetOfParticles(imgSet, starFile, stackFile):
""" This function will write a SetOfImages as Bsoft metadata.
Params:
imgSet: the SetOfImages instance.
starFile: the filename where to write the metadata.
"""
mdata = md.MetaData()
mdata.setColumnFormat(False)
imgRow = mdata.Row()
imgRow.setValue("micrograph.id", int(1))
imgRow.setValue("particle.x_origin", str(stackFile))
imgRow.writeToMd(mdata, mdata.addObject())
imgSet._bsoftStar = String(starFile)
def createOutput(self):
fnStruct = glob.glob(self._getExtraPath("atomStructIn*"))[0]
for fnDir in glob.glob(self._getPath('glide-*')):
fnBase = os.path.split(fnDir)[1]
fnGrid = os.path.join(fnDir, '%s.zip' % fnBase)
if os.path.exists(fnGrid):
gridFile = SchrodingerGrid(filename=fnGrid)
gridFile.structureFile = String(fnStruct)
n = fnDir.split('glide-')[1]
outputDict = {'outputGrid%s' % n: gridFile}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.inputStructure, gridFile)
def sortImages(self, inputId):
imagesMd = self._getPath('images.xmd')
writeSetOfParticles(self.inputParticles.get(), imagesMd)
args = "-i Particles@%s --addToInput " % imagesMd
if self.autoParRejection == self.REJ_MAXZSCORE:
args += "--zcut " + str(self.maxZscore.get())
elif self.autoParRejection == self.REJ_PERCENTAGE:
args += "--percent " + str(self.percentage.get())
self.runJob("xmipp_image_sort_by_statistics", args)
self.outputMd = String(imagesMd)
def saveConfig(filename):
from pyworkflow.mapper import SqliteMapper
from pyworkflow.object import String, Integer
mapper = SqliteMapper(filename)
o = Config()
for k, v in globals().iteritems():
if k.startswith('cfg'):
if type(v) is str:
value = String(v)
else:
value = Integer(v)
setattr(o, k, value)
mapper.insert(o)
mapper.commit()
def createChimeraScript(self, volume, pdb):
""" Create a chimera script to visualize a pseudoatoms pdb
obteined from a given EM 3d volume.
A property will be set in the pdb object to
store the location of the script.
"""
pseudoatoms = pdb.getFileName()
scriptFile = pseudoatoms + '_chimera.cmd'
pdb._chimeraScript = String(scriptFile)
sampling = volume.getSamplingRate()
radius = sampling * self.pseudoAtomRadius.get()
fnIn = getImageLocation(volume)
if fnIn.endswith(":mrc"):
fnIn = fnIn[:-4]
x, y, z = volume.getOrigin(force=True).getShifts()
xx, yy, zz = volume.getDim()
dim = volume.getDim()[0]
bildFileName = os.path.abspath(self._getExtraPath("axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fhCmd = open(scriptFile, 'w')
fhCmd.write("open %s\n" % basename(pseudoatoms))
fhCmd.write("rangecol bfactor,a 0 white 1 red\n")
fhCmd.write("setattr a radius %f\n" % radius)
fhCmd.write("represent sphere\n")
fhCmd.write("open %s\n" % abspath(fnIn))
threshold = 0.01
if self.maskMode == NMA_MASK_THRE:
self.maskThreshold.get()
# set sampling
fhCmd.write("volume #1 level %f transparency 0.5 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n" % (threshold, sampling, x, y, z))
fhCmd.write("open %s\n" % bildFileName)
#fhCmd.write("move %0.2f,%0.2f,%0.2f model #0 coord #2\n"
# % ((xx / 2. * sampling) - xv,
# (yy / 2. * sampling) - yv,
# (zz / 2. * sampling) - zv))
fhCmd.write("move %0.2f,%0.2f,%0.2f model #0 coord #2\n" %
(x + (xx / 2. * sampling), y + (yy / 2. * sampling), z +
(zz / 2. * sampling)))
fhCmd.close()
def createOutputSingle(self, fnSite, fnStructureFile, score, dscore,
srcObj):
n = fnSite.split('@')[0]
fnDir = self._getPath("grid-%s" % n)
if os.path.exists(fnDir):
fnBase = os.path.split(fnDir)[1]
fnGrid = os.path.join(fnDir, '%s.zip' % fnBase)
if os.path.exists(fnGrid):
gridFile = SchrodingerGrid(filename=fnGrid)
gridFile.structureFile = String(fnStructureFile)
gridFile.bindingSiteScore = Float(score)
gridFile.bindingSiteDScore = Float(dscore)
n = fnDir.split('grid-')[1]
outputDict = {'outputGrid%s' % n: gridFile}
self._defineOutputs(**outputDict)
self._defineSourceRelation(srcObj, gridFile)
def show(self, form, *params):
protocol = form.protocol
try:
models = self.getModelsChainsStep(protocol)
except Exception as e:
print "ERROR: ", e.message
return
self.editionListOfChains(models)
finalChainList = []
for i in self.chainList:
finalChainList.append(String(i))
provider = ListTreeProviderString(finalChainList)
dlg = dialog.ListDialog(
form.root, "Model chains", provider,
"Select one of the chains (model, chain, "
"number of chain residues)")
form.setVar('inputStructureChain', dlg.values[0].get())
def _updateParticle(self, item, row):
item.setClassId(row.rlnClassNumber)
self._reader.setParticleTransform(item, row)
# Try to create extra objects only once if item is reused
if not hasattr(item, '_rlnNormCorrection'):
item._rlnNormCorrection = Float()
item._rlnLogLikeliContribution = Float()
item._rlnMaxValueProbDistribution = Float()
item._rlnNormCorrection.set(row.rlnNormCorrection)
item._rlnLogLikeliContribution.set(row.rlnLogLikeliContribution)
item._rlnMaxValueProbDistribution.set(row.rlnMaxValueProbDistribution)
if hasattr(item, '_rlnGroupName'):
item._rlnGroupName.set(row.rlnGroupName)
elif hasattr(row, 'rlnGroupName'):
item._rlnGroupName = String(row.rlnGroupName)
def __init__(self, **kwargs):
OrderedObject.__init__(self, **kwargs)
self.name = String()
# Number of cores from which the queue is mandatory
# 0 means no mandatory at all
# 1 will force to launch all jobs through the queue
self.mandatory = Integer()
self.queues = None # List for queue configurations
self.submitCommand = String()
# Allow to change the prefix of submission scripts
# we used by default the ID.job, but in some clusters
# the job script should start by a letter
self.submitPrefix = String()
self.checkCommand = String()
self.cancelCommand = String()
self.submitTemplate = String()
self.jobDoneRegex = String()
def denoiseImages(self, inputId, inputClassesId):
# We start preparing writing those elements we're using as input to keep them untouched
imagesMd = self._getPath('images.xmd')
writeSetOfParticles(self.inputParticles.get(), imagesMd)
classesMd = self._getPath('classes.xmd')
writeSetOfClasses2D(self.inputClasses.get(), classesMd)
fnRoot = self._getExtraPath('pca')
fnRootDenoised = self._getExtraPath('imagesDenoised')
args = '-i Particles@%s --oroot %s --eigenvectors %d --maxImages %d' % (imagesMd, fnRoot, self.maxPCABases.get(), self.maxClasses.get())
self.runJob("xmipp_image_rotational_pca", args)
N=min(self.maxPCABases.get(), self.PCABases2Project.get())
args='-i %s -o %s.stk --save_metadata_stack %s.xmd --basis %s.stk %d'\
% (imagesMd, fnRootDenoised, fnRootDenoised, fnRoot, N)
self.runJob("xmipp_transform_filter", args)
self.outputMd = String('%s.stk' % fnRootDenoised)
def createOutputStep(self):
outputVols = self._createSetOfVolumes()
for i, vol in enumerate(self._iterInputVols()):
volume = vol.clone()
volDir = self._getVolDir(i+1)
volPrefix = 'vol%03d_' % (i+1)
validationMd = self._getExtraPath(volPrefix + 'validation.xmd')
moveFile(join(volDir, 'validation.xmd'),
validationMd)
clusterMd = self._getExtraPath(volPrefix + 'clusteringTendency.xmd')
moveFile(join(volDir, 'clusteringTendency.xmd'), clusterMd)
md = xmipp.MetaData(validationMd)
weight = md.getValue(xmipp.MDL_WEIGHT, md.firstObject())
volume.weight = Float(weight)
volume.clusterMd = String(clusterMd)
volume.cleanObjId() # clean objects id to assign new ones inside the set
outputVols.append(volume)
outputVols.setSamplingRate(volume.getSamplingRate())
self._defineOutputs(outputVolumes=outputVols)
def _defineParams(self, form, fullForm=True):
self._defineParams1(form,"t","Cp")
if fullForm:
form.addParam('fitType', params.EnumParam, choices=["Linear","Logarithmic","Relative"], label="Fit mode", default=1,
help='Linear: sum (Cobserved-Cpredicted)^2\nLogarithmic: sum(log10(Cobserved)-log10(Cpredicted))^2\n'\
"Relative: sum ((Cobserved-Cpredicted)/Cobserved)^2")
form.addParam('Nexp', params.IntParam, label="Number of exponentials", default=1,
help='Number of exponentials to fit')
else:
self.fitType=Integer()
self.fitType.set(1)
self.Nexp=Integer()
self.Nexp.set(1)
form.addParam('bounds', params.StringParam, label="Amplitude and time constant bounds", default="", expertLevel=LEVEL_ADVANCED,
help='Bounds for the c_i amplitudes and lambdas.\nExample 1: (0,10);(0,1e-2) -> c1 in (0,10), lambda1 in (0,1e-2)\n'\
'Example 2: (0,10);(0,1e-2);(0,1);(0,1e-1) -> c1 in (0,10), lambda1 in (0,1e-2), c2 in (0,1), lambda2 in (0,1e-1)')
form.addParam('confidenceInterval', params.FloatParam, label="Confidence interval=", default=95, expertLevel=LEVEL_ADVANCED,
help='Confidence interval for the fitted parameters')
if fullForm:
form.addParam('reportX', params.StringParam, label="Evaluate at X=", default="", expertLevel=LEVEL_ADVANCED,
help='Evaluate the model at these X values\nExample 1: [0,5,10,20,40,100]\nExample 2: 0:0.55:10, from 0 to 10 in steps of 0.5')
else:
self.reportX=String()
self.reportX.set("")
def getTemplate(root):
# Check if there is any .json.template in the template folder
# get the template folder
templateFolder = pw.getTemplatePath()
# Get all ".json.template" there
templates = []
for file in glob.glob1(templateFolder, "*.json.template"):
templates.append(String(file))
if len(templates):
if len(templates) == 1:
chosen = templates[0].get()
else:
provider = ListTreeProviderString(templates)
dlg = dialog.ListDialog(root, "Workflow templates", provider,
"Select one of the templates.")
chosen = dlg.values[0].get()
chosen = os.path.join(templateFolder, chosen)
print("Template to use: %s" % chosen)
with open(chosen, 'r') as myfile:
template = myfile.read()
# Replace environment variables
template = template % os.environ
return template
else:
raise Exception("There isn't any *.json.template at %s" % templates)
