still fighting py2 vs py3

py/mains/map_queue_template.py

@@ -15,7 +15,7 @@ for i in np.arange(30):
   q.put(i)
 
 def f(x):
-    global zz 
+    global zz
     try:
       a=q.get() # get one more element
       zz = zz+1
@@ -26,8 +26,7 @@ def f(x):
 
 if __name__ == '__main__':
     p = Pool(5)
-      
-    a=p.map(f,np.arange(30) )
+
+    a=list(p.map(f,np.arange(30) ))
     print ">>>",a
     print "zz=",zz
-

py/mains/print_tbd.py

@@ -57,7 +57,7 @@ def process(args):
         sys.exit()
 
     for i in range(data.size/3):
-        print (' '.join(map(str,data[:,i])))
+        print (' '.join(list(map(str,data[:,i]))))
 
 
 # -----------------------------------------------------

py/mains/uns_extract_halo.py

 #!/usr/bin/env python
 
 import sys
-from uns_simu import *
-from simulations.ccod import * 
+import unsio
+from unsiotools.uns_simu import *
+from unsiotools.simulations import csnapshot
+from unsiotools.simulations import ccod
 import argparse
-
-sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+import numpy as np
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-# commandLine, parse the command line 
+# commandLine, parse the command line
 def commandLine():
     dbname=None
     ncores=None
@@ -19,7 +20,9 @@ def commandLine():
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     # options
     parser.add_argument('simname', help='Simulation name')
-    parser.add_argument('haloN', help='Selected component')
+    parser.add_argument('input', help='UNS input file')
+    parser.add_argument('output', help='Nemo output file')
+    parser.add_argument('haloN', help='Select halo number (1 or 2)',type=int)
     parser.add_argument('--dbname',help='UNS database file name', default=dbname)
     parser.add_argument('--verbose',help='verbose mode', default=False)
 
@@ -33,9 +36,57 @@ def commandLine():
 # -----------------------------------------------------
 # process, is the core function
 def process(args):
-    
-    pass
-    
+
+    cod=ccod.CCod(args.simname,verbose_debug=args.verbose)
+    if cod.isMultipleHalo():
+        print("Muliple halo = ",cod.isMultipleHalo())
+        uns_snap=csnapshot.CSnapshot(args.input,"halo")
+        ok = uns_snap.nextFrame()
+        if ok:
+            select="halo"
+            ok,timex=uns_snap.getData("time")
+            print("timex=",timex,type(timex))
+            ok,pos=uns_snap.getData(select,"pos")
+            ok,mass=uns_snap.getData(select,"mass")
+            ok,vel =uns_snap.getData(select,"vel")
+            ok,id=uns_snap.getData(select,"id")
+            ok,mass,pos,vel = cod.getExtractHalo(id,mass,pos,vel,args.haloN)
+            print(mass,pos,vel)
+            unso=unsio.CunsOut(args.output,"nemo")
+            unso.setValueF("time",timex)
+            unso.setArrayF("all","pos",pos)
+            unso.setArrayF("all","mass",mass)
+            unso.setArrayF("all","vel",vel)
+            unso.save()
+        else:
+            print("Unable to load data from [%s]"%(agrs.snapshot))
+    else :
+        print("No multiple halo detected for simulation [%s]"%(args.simname))
+
+
+
+
+#
+# ----
+#
+def extractHalo(self,id,mass,pos,vel):
+    id_sort=np.argsort(id) # sort according to ID order
+    offset=0
+    myidsort=np.zeros(1)
+    if self.__halo_N==1:   # first halo
+        mylast=self.__halo_part[0]
+        myidsort = id_sort[0:mylast]
+    else :                 # second halo
+        mylast=self.__halo_part[1]
+        offset = self.__halo_part[0]+mylast
+        myidsort = id_sort[self.__halo_part[0]:offset]
+    #print("myidsort : ",myidsort,mylast,self.__halo_part)
+    pos = np.reshape(pos,(-1,3)) # reshape pos to nbody,3
+    pos = np.reshape(pos[myidsort],-1) # select ids
+    vel = np.reshape(vel,(-1,3)) # reshape vel to nbody,3
+    vel = np.reshape(vel[myidsort],-1) # select ids
+
+    return True,mass[myidsort],pos,vel
 
 # -----------------------------------------------------
 # main program

py/unsiotools/simulations/c2dplot.py

@@ -193,7 +193,7 @@ class C2dplot:
             try:
                 f=open(t_file,"r")
                 while True:
-                    atime=map(np.float,(f.readline().split()))
+                    atime=list(map(np.float,(f.readline().split())))
                     if (len(atime)>0):
                         if (atime[0]-0.001)<time and (atime[0]+0.001)>time:
                             f.close()
@@ -540,13 +540,14 @@ class C2dplot:
         if ok:
             # get data
             ok,rho=uns.getData(comp,"rho") # rho
+
             if not ok:
-                rho=np.ones(pos.size/3)
+                rho=np.ones(int(pos.size/3))
 
             # get data
             ok,mass=uns.getData(comp  ,"mass") # gas density
             if not ok:
-                mass=np.ones(pos.size/3)
+                mass=np.ones(int(pos.size/3))
 
             # reshape array in x,y,z arrays
             pos=np.reshape(pos,(-1,3))        # pos reshaped in a 2D array [nbody,3]
@@ -777,7 +778,6 @@ class C2dplot:
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # commandLine, parse the command line
 def commandLine():
-
     import argparse
     # help
     parser = argparse.ArgumentParser(description="Display 2D image from UNS data",
@@ -812,7 +812,7 @@ def commandLine():
     args = parser.parse_args()
 
     if args.cmap=="show": # show colormap
-        import general.ctools as ct
+        import unsiotools.general.ctools as ct
         ct.displayColormap()
         sys.exit()
 
@@ -845,7 +845,9 @@ def process(args):
 #        else:
 #            print ("[%s] is not a UNS snapshot ..."%(simname))
     except Exception as x :
+        import traceback
         print (x,file=sys.stderr)
+        traceback.print_exc(file=sys.stdout)
     except KeyboardInterrupt:
         sys.exit()
 
@@ -853,4 +855,4 @@ def process(args):
 # -----------------------------------------------------
 # main program
 if __name__ == '__main__':
-  commandLine()
+    commandLine()

py/unsiotools/simulations/ccod.py

@@ -20,7 +20,6 @@ import signal
 
 import matplotlib.pyplot as plt
 
-
 #
 # ----
 #
@@ -35,7 +34,7 @@ class CCod:
     __cod_file_base=None
     __ctree_threshold=10000
     __fastcod=True
-    __halo_part=np.zeros(10)
+    __halo_part=np.zeros(10,dtype=int)
     __is_multiple_halo=False
     __ok_halo_N=False
     __halo_comp=None
@@ -357,6 +356,12 @@ class CCod:
     #
     # ----
     #
+    def getExtractHalo(self,id,mass,pos,vel, halo_id):
+        self.__halo_N=halo_id
+        return self.__extractHalo(id,mass,pos,vel)
+    #
+    # ----
+    #
     def __extractHalo(self,id,mass,pos,vel):
         id_sort=np.argsort(id) # sort according to ID order
         offset=0
@@ -368,7 +373,6 @@ class CCod:
             mylast=self.__halo_part[1]
             offset = self.__halo_part[0]+mylast
             myidsort = id_sort[self.__halo_part[0]:offset]
-        #print("myidsort : ",myidsort,mylast,self.__halo_part)
         pos = np.reshape(pos,(-1,3)) # reshape pos to nbody,3
         pos = np.reshape(pos[myidsort],-1) # select ids
         vel = np.reshape(vel,(-1,3)) # reshape vel to nbody,3
@@ -417,11 +421,8 @@ class CCod:
             print("\n\n!!! File [%s] does not exist !!!!\n\n"%(model_param),file=sys.stderr)
         self.__halo_part=self.__halo_part[np.where(self.__halo_part>0)]
         if self.__vdebug:
-            print (self.__halo_part,self.__halo_part.size,file=sys.stderr)
+            print (">>> ",self.__halo_part,self.__halo_part.size,file=sys.stderr)
         return ok
-
-
-
     #
     # ----
     # Compute mering time between two halos galaxy
@@ -581,9 +582,9 @@ class CCod:
             f=open(cod_file,"r")
             try:
                 while True:
-                    tcxv=map(np.float64,(f.readline().split()))
+                    tcxv=list(map(np.float64,(f.readline().split())))
                     #print ("TCXV =",n,tcxv,len(tcxv))
-                    if (len(tcxv)>0):
+                    if (len(tcxv)>0):                    
                         atime=tcxv[0]
                         if (atime-0.001)<time and (atime+0.001)>time:
                             return True,tcxv

py/unsiotools/simulations/ccom.py

@@ -3,7 +3,7 @@ from __future__ import print_function
 from ..uns_simu import *
 from .csnapshot import *
 from .cfalcon import *
-from .ctree import * 
+from .ctree import *
 
 from multiprocessing import Process, Lock,Pool
 import multiprocessing
@@ -209,7 +209,7 @@ class CCom:
                     xx=f.readline()
                     if (len(xx)>0):
                         tcxv.append( np.float64(xx))
-                        tcxv.append(map(np.float64,(f.readline().split())))
+                        tcxv.append(list(map(np.float64,(f.readline().split()))))
                         if (len(tcxv)>0):
                             atime=tcxv[0]
                             read_index=tcxv[1][0]

py/unsiotools/simulations/cinert.py

@@ -517,7 +517,7 @@ class CInert:
             try:
                 f=open(t_file,"r")
                 while True:
-                    atime=map(np.float,(f.readline().split()))
+                    atime=list(map(np.float,(f.readline().split())))
                     if (len(atime)>0):
                         if (atime[0]-0.001)<time and (atime[0]+0.001)>time:
                             f.close()

py/unsiotools/simulations/cmovie.py

@@ -151,7 +151,7 @@ class CMovie:
             try:
                 f=open(t_file,"r")
                 while True:
-                    atime=map(np.float,(f.readline().split()))
+                    atime=list(map(np.float,(f.readline().split())))
                     if (len(atime)>0):
                         if (atime[0]-0.001)<time and (atime[0]+0.001)>time:
                             f.close()
@@ -309,7 +309,7 @@ class CMovie:
             try:
                 f=open(t_file,"r")
                 while True:
-                    atime=map(np.float,(f.readline().split()))
+                    atime=list(map(np.float,(f.readline().split())))
                     if (len(atime)>0):
                         if (atime[0]-0.001)<time and (atime[0]+0.001)>time:
                             f.close()

py/unsiotools/simulations/cplotinert.py

-#!/usr/bin/python
+#!/usr/bin/env python
 from __future__ import print_function
 from ..uns_simu import *
 
@@ -76,7 +76,7 @@ class CPlotInert:
             f.readline() #skip time
             icut=0
             #try:
-            myline=map(np.float,(f.readline().split()))
+            myline=list(map(np.float,(f.readline().split())))
             #print(myline)
             lambda1=myline[10]
             lambda2=myline[11]
@@ -117,13 +117,20 @@ class CPlotInert:
         #!!gs = gridspec.GridSpec(1, 2,wspace=0,hspace=0,width_ratios=[2,2],height_ratios=[1,1])#height_ratios=h,width_ratios=w)
         #print(gs.get_width_ratios(),gs.get_height_ratios(),gs.get_grid_positions(fig))
         #!!fig.suptitle("%s %s"%(self.__simname,self.__component))
+        import os
         allres=sorted(glob.glob(self.__dir_moi+"/inertia_*"))
+        # keep only directories
+        allresdir=[]
+        for d in allres:
+            if os.path.isdir(d):
+                allresdir.append(d)
 
-        fig,axes = plt.subplots(ncols=len(allres),sharey=False,figsize=(12, 6))#gridspec_kw={'width_ratios': [2, 2]})
+
+        fig,axes = plt.subplots(ncols=len(allresdir),sharey=False,figsize=(12, 6))#gridspec_kw={'width_ratios': [2, 2]})
         fig.suptitle("%s %s"%(self.__simname,self.__component))
 
         n=0
-        for res in allres:
+        for res in allresdir:
             #ax = plt.subplot(gs[0,n])
             ax= axes[n]
             ax.set_xlabel("Gyears")

py/unsiotools/simulations/crectify.py

@@ -219,7 +219,7 @@ class CRectify:
             try:
                 f=open(eigen_file,"r")
                 while True:
-                    tce=map(np.float64,(f.readline().split()))
+                    tce=list(map(np.float64,(f.readline().split())))
                     if (len(tce)>0):
                         atime=tce[0]
                         if (atime-0.001)<time and (atime+0.001)>time:
@@ -355,7 +355,7 @@ class CRectify:
             f=open(rect_file,"r")
             try:
                 while True:
-                    data=map(np.float64,(f.readline().split()))
+                    data=list(map(np.float64,(f.readline().split())))
                     #print ("DATA =",n,data,len(data))
                     if (len(data)>0):
                         atime=data[0]

py/unsiotools/simulations/csnapshot.py

@@ -152,10 +152,10 @@ class CSnapshot:
                 if type==2: # array
                     ret_data = np.append(ret_data,data)
                 else:
-                    ret_data = data[0]
+                    ret_data = data
             else:
                 status=0 # one component missing
-            if self.__vdebug:
+            if self.__vdebug and type==2:
                 print ("ok=",ok," data=",data.size," ret_data=",ret_data.size)
         return status,ret_data
 #
@@ -173,13 +173,15 @@ class CSnapshot:
             # proceed __uns.getValue()
             if tab_value_F.count(comp_value) > 0:
                 ok,ret_data[0]=self.__uns.getValueF(comp_value)
+                data=float(ret_data[0])
             else:
                 if tab_value_I.count(comp_value) > 0:
                     ok,ret_data[0]=self.__uns.getValueI(comp_value)
+                    data=int(ret_data[0])
             #ret_data[0]=data
             if self.__vdebug:
                 print ("ok,data",ok,data)
-            return ok,1,ret_data
+            return ok,1,data
         else:
             if tag != "id":
                 ok,data=self.__uns.getArrayF(comp_value,tag)
@@ -216,7 +218,7 @@ class CSnapshot:
             if com: # resquest com
                 ok,mass=self.getData(select,"mass") # get mass
                 if not ok: # no mass
-                    mass=np.ones(pos.size/3) # fake mass
+                    mass=np.ones(int(pos.size/3)) # fake mass
                 cxv=self.center(pos,None,mass,True) # centering
             # reshape pos 1d array to 2d array [nbody,3]
             pos2d=np.reshape(pos,(-1,3))

setup.py

@@ -138,7 +138,7 @@ def setup_package():
         platforms=["Linux", "Mac OS-X", "Unix"],
         python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*',
         package_dir={'':'py'}, # all packages are under 'py' directory
-        packages=['unsiotools', 'unsiotools/simulations'],
+        packages=['unsiotools', 'unsiotools/simulations','unsiotools/general'],
         cmdclass={'build_py': build_py},
         py_modules=['unsiotools/py_unstools'],
         ext_modules = [
@@ -175,6 +175,9 @@ def setup_package():
                                             os.environ['NEMO']+'/usr/dehnen/falcON/lib' ]
             )
         ],
+        scripts=[
+            'py/mains/uns_extract_halo.py',
+        ],
         entry_points={
             "console_scripts": [
                 "uns_2dplot.py   = unsiotools.simulations.c2dplot:commandLine",
@@ -187,8 +190,8 @@ def setup_package():
                 "processing_analysis.py  = unsiotools.simulations.cuns_analysis:commandLine",
             ],
         },
-        #install_requires=['numpy'],
-        #setup_requires=['numpy']
+        install_requires=['python-unsio','matplotlib','scipy','numpy'],
+        setup_requires=['numpy']
     )
     setup(**metadata)
     #