def insertAffinityPropagationRun(self, classes):
### Preliminary data
numclass = len(classes.keys())
projectid = apProject.getProjectIdFromAlignStackId(self.params['alignstackid'])
alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
pathdata = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### Affinity Propagation Params object
affpropq = appiondata.ApAffinityPropagationClusterParamsData()
affpropq['mask_diam'] = 2.0*self.params['maskrad']
affpropq['run_seconds'] = time.time()-self.t0
affpropq['preference_type'] = self.params['preftype']
### Align Analysis Run object
analysisq = appiondata.ApAlignAnalysisRunData()
analysisq['runname'] = self.params['runname']
analysisq['path'] = pathdata
analysisq['description'] = self.params['description']
analysisq['alignstack'] = alignstackdata
analysisq['hidden'] = False
### linked through cluster not analysis
### Clustering Run object
clusterrunq = appiondata.ApClusteringRunData()
clusterrunq['runname'] = self.params['runname']
clusterrunq['description'] = self.params['description']
clusterrunq['boxsize'] = alignstackdata['boxsize']
clusterrunq['pixelsize'] = alignstackdata['pixelsize']
clusterrunq['num_particles'] = self.params['numpart']
clusterrunq['alignstack'] = alignstackdata
clusterrunq['analysisrun'] = analysisq
clusterrunq['affpropparams'] = affpropq
### Clustering Stack object
clusterstackq = appiondata.ApClusteringStackData()
clusterstackq['avg_imagicfile'] = "classaverage-"+self.timestamp+".hed"
clusterstackq['num_classes'] = numclass
clusterstackq['clusterrun'] = clusterrunq
clusterstackq['path'] = pathdata
clusterstackq['hidden'] = False
imagicfile = os.path.join(self.params['rundir'], clusterstackq['avg_imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find average stack file: "+imagicfile)
### looping over clusters
apDisplay.printColor("Inserting particle classification data, please wait", "cyan")
for i,classkey in enumerate(classes.keys()):
classnum = i+1
partlist = classes[classkey]
#print "MINIMUM: ", min(partlist)
classroot = "%s.%d"% (self.timestamp, classnum-1)
classdocfile = os.path.join(self.params['rundir'], classroot)
### Clustering Particle object
clusterrefq = appiondata.ApClusteringReferenceData()
clusterrefq['refnum'] = classnum
clusterrefq['clusterrun'] = clusterrunq
clusterrefq['path'] = pathdata
clusterrefq['num_particles'] = len(partlist)
#clusterrefq['ssnr_resolution'] = self.cluster_resolution[i]
### looping over particles
sys.stderr.write(".")
for partnum in partlist:
alignpartdata = self.getAlignParticleData(partnum, alignstackdata)
### Clustering Particle objects
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = clusterstackq
clusterpartq['alignparticle'] = alignpartdata
clusterpartq['partnum'] = partnum
clusterpartq['refnum'] = classnum
clusterpartq['clusterreference'] = clusterrefq
### finally we can insert parameters
if self.params['commit'] is True:
clusterpartq.insert()
return
def insertRotKerDenSOM(self):
inserttime = time.time()
### Preliminary data
projectid = apProject.getProjectIdFromAlignStackId(self.params['alignstackid'])
alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
numclass = self.params['xdim']*self.params['ydim']
pathdata = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### rotKerDen SOM Params object
rotkerdenson = appiondata.ApRotKerDenSOMParamsData()
#rotkerdenson['mask_diam'] = 2.0*self.params['maskrad']
rotkerdenson['x_dimension'] = self.params['xdim']
rotkerdenson['y_dimension'] = self.params['ydim']
#rotkerdenson['convergence'] = self.params['converge']
rotkerdenson['run_seconds'] = time.time()-self.t0
rotkerdenson['initregulfact'] = self.params['initregulfact']
rotkerdenson['finalregulfact'] = self.params['finalregulfact']
rotkerdenson['incrementregulfact'] = self.params['incrementregulfact']
rotkerdenson['spectrainnerradius'] = self.params['spectrainnerradius']
rotkerdenson['spectraouterradius'] = self.params['spectraouterradius']
rotkerdenson['spectralowharmonic'] = self.params['spectralowharmonic']
rotkerdenson['spectrahighharmonic'] = self.params['spectrahighharmonic']
### Analysis Run object
analysisq = appiondata.ApAlignAnalysisRunData()
analysisq['runname'] = self.params['runname']
analysisq['path'] = pathdata
analysisq['description'] = self.params['description']
analysisq['alignstack'] = alignstackdata
analysisq['hidden'] = False
### Clustering Run object
clusterrunq = appiondata.ApClusteringRunData()
clusterrunq['runname'] = self.params['runname']
clusterrunq['description'] = self.params['description']
clusterrunq['boxsize'] = alignstackdata['boxsize']
clusterrunq['pixelsize'] = alignstackdata['pixelsize']
clusterrunq['num_particles'] = self.params['numpart']
clusterrunq['alignstack'] = alignstackdata
clusterrunq['analysisrun'] = analysisq
clusterrunq['rotkerdenparams'] = rotkerdenson
### Clustering Stack object
#Stack with cluster averages??????
template =os.path.join(self.params['rundir'],self.spectraTemporalFilesMask + ".png")
files = glob.glob(template)
imglist = []
for listname in files:
a=apImage.readPNG(listname)
imglist.append(a)
apImagicFile.writeImagic(imglist,"rotkerdenstack" +self.timestamp + ".hed")
clusterstackq = appiondata.ApClusteringStackData()
clusterstackq['avg_imagicfile'] = "rotkerdenstack"+self.timestamp+".hed"
clusterstackq['num_classes'] = numclass
clusterstackq['clusterrun'] = clusterrunq
clusterstackq['path'] = pathdata
clusterstackq['hidden'] = False
imagicfile = os.path.join(self.params['rundir'], clusterstackq['avg_imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find average stack file: "+imagicfile)
### looping over clusters
apDisplay.printColor("Inserting particle classification data, please wait", "cyan")
numclass = self.params['xdim']*self.params['ydim']
for i in range(numclass):
classnum = i+1
classroot = "%s.%d"% (self.timestamp, classnum-1)
classdocfile = os.path.join(self.params['rundir'], classroot)
partlist = self.readClassDocFile(classdocfile)
### Clustering Particle object
# MRC image for each code node but plot or image
clusterrefq = appiondata.ApClusteringReferenceData()
clusterrefq['refnum'] = classnum
clusterrefq['avg_mrcfile'] = classroot+".mrc"
clusterrefq['clusterrun'] = clusterrunq
clusterrefq['path'] = pathdata
clusterrefq['num_particles'] = len(partlist)
### looping over particles
#which particles belong to which code node
sys.stderr.write(".")
for partnum in partlist:
alignpartdata = self.getAlignParticleData(partnum, alignstackdata)
### Clustering Particle objects
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = clusterstackq
clusterpartq['alignparticle'] = alignpartdata
clusterpartq['partnum'] = partnum
clusterpartq['refnum'] = classnum
clusterpartq['clusterreference'] = clusterrefq
### finally we can insert parameters
if self.params['commit'] is True:
clusterpartq.insert()
sys.stderr.write("\n")
apDisplay.printMsg("Insertion complete in %s"%(apDisplay.timeString(time.time()-inserttime)))
def insertKerDenSOM(self, binned=None):
### Preliminary data
projectid = apProject.getProjectIdFromAlignStackId(self.params['alignstackid'])
alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
numclass = self.params['xdim']*self.params['ydim']
pathdata = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### KerDen SOM Params object
kerdenq = appiondata.ApKerDenSOMParamsData()
kerdenq['mask_diam'] = 2.0*self.params['maskrad']
kerdenq['x_dimension'] = self.params['xdim']
kerdenq['y_dimension'] = self.params['ydim']
kerdenq['convergence'] = self.params['converge']
kerdenq['run_seconds'] = time.time()-self.t0
### Align Analysis Run object
analysisq = appiondata.ApAlignAnalysisRunData()
analysisq['runname'] = self.params['runname']
analysisq['path'] = pathdata
analysisq['description'] = self.params['description']
analysisq['alignstack'] = alignstackdata
analysisq['hidden'] = False
### linked through cluster not analysis
#analysisq['kerdenparams'] = kerdenq
### Clustering Run object
clusterrunq = appiondata.ApClusteringRunData()
clusterrunq['runname'] = self.params['runname']
clusterrunq['description'] = self.params['description']
# what if we binned the aligned stack to get the new one
if binned is None:
boxsize = alignstackdata['boxsize']
pixelsize = alignstackdata['pixelsize']
else:
boxsize = alignstackdata['boxsize'] / binned
pixelsize = alignstackdata['pixelsize'] * binned
clusterrunq['boxsize'] = boxsize
clusterrunq['pixelsize'] = pixelsize
clusterrunq['num_particles'] = self.params['numpart']
clusterrunq['alignstack'] = alignstackdata
clusterrunq['analysisrun'] = analysisq
clusterrunq['kerdenparams'] = kerdenq
### Clustering Stack object
clusterstackq = appiondata.ApClusteringStackData()
clusterstackq['avg_imagicfile'] = "kerdenstack"+self.timestamp+".hed"
clusterstackq['num_classes'] = numclass
clusterstackq['clusterrun'] = clusterrunq
clusterstackq['path'] = pathdata
clusterstackq['hidden'] = False
imagicfile = os.path.join(self.params['rundir'], clusterstackq['avg_imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find average stack file: "+imagicfile)
### looping over clusters
apDisplay.printColor("Inserting particle classification data, please wait", "cyan")
for i in range(numclass):
classnum = i+1
classroot = "%s.%d"% (self.timestamp, classnum-1)
classdocfile = os.path.join(self.params['rundir'], classroot)
partlist = self.readClassDocFile(classdocfile)
### Clustering Particle object
clusterrefq = appiondata.ApClusteringReferenceData()
clusterrefq['refnum'] = classnum
clusterrefq['avg_mrcfile'] = classroot+".mrc"
clusterrefq['clusterrun'] = clusterrunq
clusterrefq['path'] = pathdata
clusterrefq['num_particles'] = len(partlist)
clusterrefq['ssnr_resolution'] = self.cluster_resolution[i]
### looping over particles
sys.stderr.write(".")
for partnum in partlist:
alignpartdata = self.getAlignParticleData(partnum, alignstackdata)
### Clustering Particle objects
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = clusterstackq
clusterpartq['alignparticle'] = alignpartdata
clusterpartq['partnum'] = partnum
clusterpartq['refnum'] = classnum
clusterpartq['clusterreference'] = clusterrefq
### finally we can insert parameters
if self.params['commit'] is True:
clusterpartq.insert()
def insertRotKerDenSOM(self):
inserttime = time.time()
### Preliminary data
projectid = apProject.getProjectIdFromAlignStackId(
self.params['alignstackid'])
alignstackdata = appiondata.ApAlignStackData.direct_query(
self.params['alignstackid'])
numclass = self.params['xdim'] * self.params['ydim']
pathdata = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
### rotKerDen SOM Params object
rotkerdenson = appiondata.ApRotKerDenSOMParamsData()
#rotkerdenson['mask_diam'] = 2.0*self.params['maskrad']
rotkerdenson['x_dimension'] = self.params['xdim']
rotkerdenson['y_dimension'] = self.params['ydim']
#rotkerdenson['convergence'] = self.params['converge']
rotkerdenson['run_seconds'] = time.time() - self.t0
rotkerdenson['initregulfact'] = self.params['initregulfact']
rotkerdenson['finalregulfact'] = self.params['finalregulfact']
rotkerdenson['incrementregulfact'] = self.params['incrementregulfact']
rotkerdenson['spectrainnerradius'] = self.params['spectrainnerradius']
rotkerdenson['spectraouterradius'] = self.params['spectraouterradius']
rotkerdenson['spectralowharmonic'] = self.params['spectralowharmonic']
rotkerdenson['spectrahighharmonic'] = self.params[
'spectrahighharmonic']
### Analysis Run object
analysisq = appiondata.ApAlignAnalysisRunData()
analysisq['runname'] = self.params['runname']
analysisq['path'] = pathdata
analysisq['description'] = self.params['description']
analysisq['alignstack'] = alignstackdata
analysisq['hidden'] = False
### Clustering Run object
clusterrunq = appiondata.ApClusteringRunData()
clusterrunq['runname'] = self.params['runname']
clusterrunq['description'] = self.params['description']
clusterrunq['boxsize'] = alignstackdata['boxsize']
clusterrunq['pixelsize'] = alignstackdata['pixelsize']
clusterrunq['num_particles'] = self.params['numpart']
clusterrunq['alignstack'] = alignstackdata
clusterrunq['analysisrun'] = analysisq
clusterrunq['rotkerdenparams'] = rotkerdenson
### Clustering Stack object
#Stack with cluster averages??????
template = os.path.join(self.params['rundir'],
self.spectraTemporalFilesMask + ".png")
files = glob.glob(template)
imglist = []
for listname in files:
a = apImage.readPNG(listname)
imglist.append(a)
apImagicFile.writeImagic(imglist,
"rotkerdenstack" + self.timestamp + ".hed")
clusterstackq = appiondata.ApClusteringStackData()
clusterstackq[
'avg_imagicfile'] = "rotkerdenstack" + self.timestamp + ".hed"
clusterstackq['num_classes'] = numclass
clusterstackq['clusterrun'] = clusterrunq
clusterstackq['path'] = pathdata
clusterstackq['hidden'] = False
imagicfile = os.path.join(self.params['rundir'],
clusterstackq['avg_imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find average stack file: " +
imagicfile)
### looping over clusters
apDisplay.printColor(
"Inserting particle classification data, please wait", "cyan")
numclass = self.params['xdim'] * self.params['ydim']
for i in range(numclass):
classnum = i + 1
classroot = "%s.%d" % (self.timestamp, classnum - 1)
classdocfile = os.path.join(self.params['rundir'], classroot)
partlist = self.readClassDocFile(classdocfile)
### Clustering Particle object
# MRC image for each code node but plot or image
clusterrefq = appiondata.ApClusteringReferenceData()
clusterrefq['refnum'] = classnum
clusterrefq['avg_mrcfile'] = classroot + ".mrc"
clusterrefq['clusterrun'] = clusterrunq
clusterrefq['path'] = pathdata
clusterrefq['num_particles'] = len(partlist)
### looping over particles
#which particles belong to which code node
sys.stderr.write(".")
for partnum in partlist:
alignpartdata = self.getAlignParticleData(
partnum, alignstackdata)
### Clustering Particle objects
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = clusterstackq
clusterpartq['alignparticle'] = alignpartdata
clusterpartq['partnum'] = partnum
clusterpartq['refnum'] = classnum
clusterpartq['clusterreference'] = clusterrefq
### finally we can insert parameters
if self.params['commit'] is True:
clusterpartq.insert()
sys.stderr.write("\n")
apDisplay.printMsg("Insertion complete in %s" %
(apDisplay.timeString(time.time() - inserttime)))
