[Swift-commit] r3155 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-10-13 12:19:07 -0500 (Tue, 13 Oct 2009)
New Revision: 3155

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/Alphasurfsim.py
Log:
for doing randomization, smoothing, clustering, getting largest value on surface data

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/Alphasurfsim.py
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/Alphasurfsim.py	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/Alphasurfsim.py	2009-10-13 17:19:07 UTC (rev 3155)
@@ -0,0 +1,159 @@
+#!/usr/bin/python
+
+import os
+import sys
+
+class AlphaSurfSim:
+
+    def __init__(self):
+        self.r_swift_args = ""
+        self.r_script = ""
+        self.permOut = ""
+        self.spec = ""
+        self.smoothwm = ""
+        self.surfsmoothOut = ""
+        self.pial = ""
+        self.maskname = ""
+        self.thresh = ""
+        self.pval = ""
+        self.rmm = ""
+        self.surfclustOut = ""
+        self.outname = ""
+        self.proc_input = ""
+        self.proc_type = ""
+        
+
+    def get_opts (self,allargstr):
+        print "length of argstr "+str(len(allargstr))
+        i = 0
+        for o in allargstr:
+            print "arg is "+o
+            if o == "--r_swift_args":
+                rstr = ""
+                j = i
+                while (allargstr[j+1].find("--")<=-1):
+                    rstr = rstr+allargstr[j+1].strip()+" "
+                    j+=1
+                self.r_swift_args= rstr
+            elif o == "--r_script":
+                self.r_script = allargstr[i+1]
+            elif o == "--permOut":
+                self.permOut = allargstr[i+1]
+            elif o == "--spec":
+                self.spec = allargstr[i+1]
+            elif o == "--smoothwm":
+                self.smoothwm = allargstr[i+1]
+            elif o == "--surfsmoothOut":
+                self.surfsmoothOut = allargstr[i+1]
+            elif o == "--pial":
+                self.pial = allargstr[i+1]
+            elif o == "--maskname":
+                self.maskname = allargstr[i+1]
+            elif o == "--thresh":
+                self.thresh = allargstr[i+1]
+            elif o == "--pval":
+                self.pval = allargstr[i+1]
+            elif o == "--rmm":
+                self.rmm = allargstr[i+1]
+            elif o == "--surfclustOut":
+                self.surfclustOut = allargstr[i+1]
+            elif o == "--proc_input":
+                self.proc_input = allargstr[i+1]
+            elif o == "--outputname":
+                self.outname = allargstr[i+1]
+            elif o == "--procedure":
+                self.proc_type = allargstr[i+1]
+            i = i+1
+    
+    def get_nodenum(self):
+        surf = open(self.pial).read().split("\n")
+        self.numnodes = surf[1].split()[0]
+        
+    def get_clstr(self):
+        cluster_file = open(self.proc_input,"r").read().split("\n")
+        cluster_file_length = len(cluster_file)-1
+        clstrlist = ""
+        for i in range(16,cluster_file_length):
+            numNd = int(cluster_file[i].split()[1])
+            clstrlist += ""+cluster_file[i].split()[0]+" "+`numNd`+"\n"
+
+        outfile = open(self.outname,"w")
+        outfile.write(clstrlist)
+        outfile.close()
+
+    def get_Perm_clstr(self):
+        cluster_file = open(self.proc_input,"r").read().split("\n")
+        cluster_file_length = len(cluster_file)-1
+        if len(cluster_file)-1 == 1:
+            clusterSize = cluster_file[0]+" \n"
+        else:
+            numNd = int(cluster_file[16].split()[1])
+            clusterSize = `numNd`+" \n"
+
+        outfile = open(self.outname,"w")
+        outfile.write(clusterSize)
+        outfile.close()
+
+    def get_clstrmass(self):
+        cluster_file = open(self.proc_input,"r").read().split("\n")
+        cluster_file_length = len(cluster_file)-1
+        clstrmasslist = ""
+        for i in range(16,cluster_file_length):
+            numNd = int(cluster_file[i].split()[1])
+            Mean = float(cluster_file[i].split()[3])
+            mass = numNd*Mean
+            massval = "%.3f" % mass
+            clstrmasslist += ""+cluster_file[i].split()[0]+" "+massval+"\n"
+
+        outfile = open(self.outname,"w")
+        outfile.write(clstrmasslist)
+        outfile.close()
+
+    def get_Perm_clstrmass(self):
+        cluster_file = open(self.proc_input,"r").read().split("\n")
+        if len(cluster_file)-1 == 1:
+            clstrmassval = cluster_file[0]+" \n"
+        else:
+            numNd = int(cluster_file[16].split()[1])
+            Mean = float(cluster_file[16].split()[3])
+            mass = numNd*Mean
+            massval = "%.3f" % mass
+            clstrmassval = massval+" \n"
+
+        outfile = open(self.outname,"w")
+        outfile.write(clstrmassval)
+        outfile.close()
+    
+    def run_r(self,proc):
+        os.environ["PROC"] = proc
+        os.environ["NUM_NODES"] = self.numnodes
+        os.environ["PERM_OUT"] = self.permOut
+        os.environ["PVAL"] = self.pval
+        os.environ["surfsmoothOut"] = self.surfsmoothOut
+        os.environ["maskname"] = self.maskname
+        os.system("R CMD BATCH --vanilla "+self.r_script)
+        pass
+        
+    def surfsmooth(self):
+        os.system("SurfSmooth -spec "+self.spec+" -surf_A "+self.smoothwm+" -met HEAT_07 -input "+self.permOut+" -target_fwhm 4 -Niter -1 -add_index -output "+self.surfsmoothOut)
+    
+    def surfclust(self):
+        os.system("SurfClust -spec "+self.spec+" -surf_A "+self.pial+" -input "+self.maskname+" 0 -rmm "+self.rmm+" -thresh_col 0 -thresh .99 -amm2 2 -sort_n_nodes -prepend_node_index -prefix "+self.surfclustOut)
+        
+        
+        
+clstr = AlphaSurfSim()
+clstr.get_opts(sys.argv)
+clstr.get_nodenum()
+clstr.run_r("genperm")
+clstr.surfsmooth()
+clstr.run_r("cutoff")
+clstr.surfclust()
+if clstr.proc_type == "NumberNodes":
+    clstr.get_clstr()
+elif clstr.proc_type == "PermNumberNodes":
+    clstr.get_Perm_clstr()
+elif clstr.proc_type == "ClusterMass":
+    clstr.get_clstrmass()
+elif clstr.proc_type == "PermClusterMass":
+    clstr.get_Perm_clstrmass()