def makeDendrogram(numfactors=1, corandata="coran/corandata", dataext=".spi"):
rundir = "cluster"
apParam.createDirectory(rundir)
### make list of factors
factorstr = ""
for fact in range(1,numfactors+1):
factorstr += str(fact)+","
factorstr = factorstr[:-1]
### do hierarchical clustering
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=True)
mySpider.toSpider(
"CL HC",
corandata+"_IMC", # path to coran data
factorstr, # factor string
)
## weight for each factor
for fact in range(numfactors):
mySpider.toSpiderQuiet("1.0")
mySpider.toSpider(
"5", #use Ward's method
"T", "5.1", rundir+"/dendrogram.ps", #dendrogram image file
"Y", rundir+"/dendrogramdoc", #dendrogram doc file
)
mySpider.close()
apImage.convertPostscriptToPng("cluster/dendrogram.ps", "dendrogram.png")
def makeDendrogram(numfactors=1, corandata="coran/corandata", dataext=".spi"):
rundir = "cluster"
apParam.createDirectory(rundir)
### make list of factors
factorstr = ""
for fact in range(1, numfactors + 1):
factorstr += str(fact) + ","
factorstr = factorstr[:-1]
### do hierarchical clustering
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=True)
mySpider.toSpider(
"CL HC",
corandata + "_IMC", # path to coran data
factorstr, # factor string
)
## weight for each factor
for fact in range(numfactors):
mySpider.toSpiderQuiet("1.0")
mySpider.toSpider(
"5", #use Ward's method
"T",
"5.1",
rundir + "/dendrogram.ps", #dendrogram image file
"Y",
rundir + "/dendrogramdoc", #dendrogram doc file
)
mySpider.close()
apImage.convertPostscriptToPng("cluster/dendrogram.ps", "dendrogram.png")
def createFactorMap(f1, f2, rundir, dataext):
### 3. factor plot
apParam.createDirectory(rundir + "/factors", warning=False)
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=False)
factorfile = rundir + "/factors/factorps" + ("%02d-%02d" % (f1, f2))
mySpider.toSpiderQuiet(
"CA SM",
"I",
rundir + "/corandata", #coran prefix
"0",
str(f1) + "," + str(f2), #factors to plot
"S",
"+",
"Y",
"5",
"0",
factorfile,
"\n\n\n\n",
"\n\n\n\n",
"\n", #9 extra steps, use defaults
)
time.sleep(2)
mySpider.close()
# hack to get postscript converted to png, require ImageMagick
apImage.convertPostscriptToPng(factorfile + ".ps",
factorfile + ".png",
size=200)
apFile.removeFile(factorfile + ".ps")
### 4. factor plot visualization
"""
### this is broken in SPIDER 13.0
mySpider = spyder.SpiderSession(dataext=dataext, logo=False)
mySpider.toSpider(
"SD C", #create coordinate file
rundir+"/corandata", #coran prefix
str(f1)+","+str(f2), #factors to plot
rundir+"/sdcdoc"+("%02d%02d" % (f1,f2)),
)
visimg = rundir+"/visimg"+("%02d%02d" % (f1,f2))
mySpider.toSpider(
"CA VIS", #visualization
"(1024,1024)",
rundir+"/sdcdoc"+("%02d%02d" % (f1,f2)), #input doc from 'sd c'
rundir+"/visdoc"+("%02d%02d" % (f1,f2)), #output doc
"alignedstack@00001", # image in series ???
"(12,12)", #num of rows, cols
"5.0", #stdev range
"(5.0,5.0)", #upper, lower thresh
visimg, #output image
"1,"+str(numpart),
"1,2",
)
mySpider.close()
emancmd = ("proc2d "+visimg+dataext+" "+visimg+".png ")
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=False)
"""
return
def hierarchClusterProcess(numpart=None,
factorlist=range(1, 5),
corandata="coran/corandata",
rundir=".",
dataext=".spi"):
"""
inputs:
coran data
number of particles
factor list
output directory
output:
dendrogram doc file
factorkey
"""
#apFile.removeFile(rundir+"/dendrogramdoc"+dataext)
factorstr, factorkey = operations.intListToString(factorlist)
dendrogramfile = rundir + "/dendrogramdoc" + factorkey + dataext
if os.path.isfile(dendrogramfile):
apDisplay.printMsg(
"Dendrogram file already exists, skipping processing " +
dendrogramfile)
return dendrogramfile
apDisplay.printMsg("Creating dendrogram file: " + dendrogramfile)
### do hierarchical clustering
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=True)
mySpider.toSpider(
"CL HC",
spyder.fileFilter(corandata) + "_IMC", # path to coran data
factorstr, # factor string
)
## weight for each factor
for fact in factorlist:
mySpider.toSpiderQuiet("1.0")
minclasssize = "%.4f" % (numpart * 0.0001 + 2.0)
mySpider.toSpider(
"5", #use Ward's method
"T",
minclasssize,
rundir + "/dendrogram.ps", #dendrogram image file
"Y",
spyder.fileFilter(dendrogramfile), #dendrogram doc file
)
mySpider.close()
if not os.path.isfile(dendrogramfile):
apDisplay.printError(
"SPIDER dendrogram creation (CL HC) failed, too many particles??")
apImage.convertPostscriptToPng("cluster/dendrogram.ps", "dendrogram.png")
return dendrogramfile
def createFactorMap(f1, f2, rundir, dataext):
### 3. factor plot
apParam.createDirectory(rundir+"/factors", warning=False)
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=False)
factorfile = rundir+"/factors/factorps"+("%02d-%02d" % (f1,f2))
mySpider.toSpiderQuiet(
"CA SM", "I",
rundir+"/corandata", #coran prefix
"0",
str(f1)+","+str(f2), #factors to plot
"S", "+", "Y",
"5", "0",
factorfile,
"\n\n\n\n","\n\n\n\n","\n", #9 extra steps, use defaults
)
time.sleep(2)
mySpider.close()
# hack to get postscript converted to png, require ImageMagick
apImage.convertPostscriptToPng(factorfile+".ps", factorfile+".png", size=200)
apFile.removeFile(factorfile+".ps")
### 4. factor plot visualization
"""
### this is broken in SPIDER 13.0
mySpider = spyder.SpiderSession(dataext=dataext, logo=False)
mySpider.toSpider(
"SD C", #create coordinate file
rundir+"/corandata", #coran prefix
str(f1)+","+str(f2), #factors to plot
rundir+"/sdcdoc"+("%02d%02d" % (f1,f2)),
)
visimg = rundir+"/visimg"+("%02d%02d" % (f1,f2))
mySpider.toSpider(
"CA VIS", #visualization
"(1024,1024)",
rundir+"/sdcdoc"+("%02d%02d" % (f1,f2)), #input doc from 'sd c'
rundir+"/visdoc"+("%02d%02d" % (f1,f2)), #output doc
"alignedstack@00001", # image in series ???
"(12,12)", #num of rows, cols
"5.0", #stdev range
"(5.0,5.0)", #upper, lower thresh
visimg, #output image
"1,"+str(numpart),
"1,2",
)
mySpider.close()
emancmd = ("proc2d "+visimg+dataext+" "+visimg+".png ")
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=False)
"""
return
def hierarchClusterProcess(numpart=None, factorlist=range(1,5),
corandata="coran/corandata", rundir=".", dataext=".spi"):
"""
inputs:
coran data
number of particles
factor list
output directory
output:
dendrogram doc file
factorkey
"""
#apFile.removeFile(rundir+"/dendrogramdoc"+dataext)
factorstr, factorkey = operations.intListToString(factorlist)
dendrogramfile = rundir+"/dendrogramdoc"+factorkey+dataext
if os.path.isfile(dendrogramfile):
apDisplay.printMsg("Dendrogram file already exists, skipping processing "+dendrogramfile)
return dendrogramfile
apDisplay.printMsg("Creating dendrogram file: "+dendrogramfile)
### do hierarchical clustering
mySpider = spyder.SpiderSession(dataext=dataext, logo=False, log=True)
mySpider.toSpider(
"CL HC",
spyder.fileFilter(corandata)+"_IMC", # path to coran data
factorstr, # factor string
)
## weight for each factor
for fact in factorlist:
mySpider.toSpiderQuiet("1.0")
minclasssize = "%.4f" % (numpart*0.0001+2.0)
mySpider.toSpider(
"5", #use Ward's method
"T", minclasssize, rundir+"/dendrogram.ps", #dendrogram image file
"Y", spyder.fileFilter(dendrogramfile), #dendrogram doc file
)
mySpider.close()
if not os.path.isfile(dendrogramfile):
apDisplay.printError("SPIDER dendrogram creation (CL HC) failed, too many particles??")
apImage.convertPostscriptToPng("cluster/dendrogram.ps", "dendrogram.png")
return dendrogramfile
