switch to unsio module

.gitignore

@@ -9,6 +9,7 @@
 
 # python
 *.pyc
+\#*
 
 # Compiled Object files
 *.slo

py/mains/add_age_to_mult4.py

 #!/usr/bin/python
 
 # unsio
-from py_unsio import *
+from unsio import *
 import numpy as np
 # cnd line
 import sys, getopt,os.path

py/mains/age_to_density.py

@@ -6,7 +6,7 @@ from __future__ import print_function
 # save stars particles to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/array_to_density.py

@@ -6,7 +6,7 @@ from __future__ import print_function
 # save stars particles to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/compare_snapshots.py

@@ -12,7 +12,7 @@ import numpy as np                # arrays are treated as numpy arrays
 import os.path
 #dirname, filename = os.path.split(os.path.abspath(__file__))
 #sys.path.append(dirname+'../modules/')  # trick to find modules directory
-from py_unsio import *
+from unsio import *
 import copy
 import tempfile
 #from IPython import embed

py/mains/decrease_nbody.py

@@ -16,8 +16,8 @@
 
 # unsio module loading
 # ==> do not forget to update PYTHONPATH environment variable with
-#     py_unsio location path
-from py_unsio import *
+#     unsio location path
+from unsio import *
 
 import numpy as np
 # cmd line

py/mains/decrease_nbody_by_rho.py

 #!/usr/bin/env python
 
-from py_unsio import *
+from unsio import *
 import numpy as np
 
 import argparse

py/mains/enzo2gadget.py

@@ -3,7 +3,7 @@
 import yt
 import numpy as np
 import sys
-from py_unsio import *
+from unsio import *
 from yt.data_objects.particle_filters import add_particle_filter
 import math
 import argparse

py/mains/gas_life.py

@@ -6,7 +6,7 @@
 
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/link_continue_snapshot.py

+#!/usr/bin/env python
+from __future__ import print_function
+import sys
+sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+import argparse
+import os,glob
+import errno
+#from uns_simu import *
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# commandLine, parse the command line
+def commandLine():
+    dbname=None
+
+    # help
+    parser = argparse.ArgumentParser(description="Link snapshot snapshot on continue MDF simulations",
+                                    formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # options
+
+    parser.add_argument('simname', help='simulation name path')
+
+    parser.add_argument('contdir', help='continuation sim dir')
+
+    parser.add_argument('--verbose',help='verbose mode on', dest="verbose", action="store_true", default=False)
+
+    # parse
+    args = parser.parse_args()
+
+    # start main funciton
+    process(args)
+
+
+# -----------------------------------------------------
+# process, is the core function
+dirname="/rudata/mdf"
+def process(args):
+    for ff in sorted(glob.glob(args.contdir+"/"+args.simname+"/SNAPS/snapshot*")):
+        try:
+            ff2,ext=ff.split(".")
+        except:
+            pass
+        base=os.path.basename(ff)
+        name,id=base.split("_")
+        try:
+            id,dummy=id.split(".")
+        except:
+            pass
+        target=dirname+"/"+args.simname+"/SNAPS/"+args.simname+"_"+id
+        if not os.path.islink(target):
+            print("target ",target)
+            print("ff =",ff)
+            try:
+                os.symlink(ff,target)
+            except OSError as e:
+                if e.errno == errno.EEXIST:
+                    try:
+                        os.remove(target)
+                        os.symlink(ff,target)
+                    except:
+                        print("unable to remove ",target)
+                else:
+                    raise e
+
+
+# -----------------------------------------------------
+# process, is the core function
+def process1(args):
+
+    snap_list =     sorted(glob.glob(args.snapshot+'_?'))
+    snap_list = snap_list+sorted(glob.glob(args.snapshot+'_??'))
+    snap_list = snap_list+sorted(glob.glob(args.snapshot+'_???'))
+    snap_list = snap_list+sorted(glob.glob(args.snapshot+'_????'))
+    snap_list = snap_list+sorted(glob.glob(args.snapshot+'_?????'))
+
+    cpt=0
+    for mysnap in snap_list:
+        mylink="snapshot_"+str(cpt)
+        if not os.path.islink(mylink):
+            print(mysnap,"snapshot_"+str(cpt))
+            os.symlink(mysnap,mylink)
+        cpt=cpt+1
+
+
+# -----------------------------------------------------
+# main program
+if __name__ == '__main__':
+    commandLine()

py/mains/mdf_build_continue.py

+#!/usr/bin/env python
+
+import sys
+from uns_simu import *
+from simulations.ccod import * 
+import argparse
+
+sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# commandLine, parse the command line 
+def commandLine():
+    dbname=None
+    ncores=None
+    fastcod=True
+    threshold=10000
+     # help
+    parser = argparse.ArgumentParser(description="Build continuation fro MDF",
+                                    formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # options
+    parser.add_argument('simname', help='Simulation name')
+    parser.add_argument('--dbname',help='UNS database file name', default=dbname)
+    parser.add_argument('--verbose',help='verbose mode', default=False)
+
+     # parse
+    args = parser.parse_args()
+
+    # start main funciton
+    process(args)
+
+
+# -----------------------------------------------------
+# process, is the core function
+def process(args):
+    
+    pass
+    
+
+# -----------------------------------------------------
+# main program
+if __name__ == '__main__':
+    commandLine()

py/mains/metal_to_density.py

@@ -6,7 +6,7 @@
 # save stars particles to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/op_file_dir.py

@@ -5,7 +5,7 @@ import sys
 sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
 
 #from py_unstools import *         # import py_unstools package
-from py_unsio import *
+from unsio import *
 from uns_simu import *
 from general.ctools import *
 import argparse

py/mains/out2uns.py

@@ -3,7 +3,7 @@ from __future__ import print_function
 
 import sys
 import numpy as np
-from py_unsio import *
+from unsio import *
 import argparse
 
 

py/mains/pot_to_density.py

@@ -6,7 +6,7 @@ from __future__ import print_function
 # save stars particles to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/process_analysis.py

@@ -9,7 +9,7 @@ import numpy as np
 import argparse
 import matplotlib
 matplotlib.use('Agg')
-#sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
 
 from simulations.cuns_analysis import *
 

py/mains/remove_sim_halo.py

@@ -5,7 +5,7 @@ import sys
 sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
 
 #from py_unstools import *         # import py_unstools package
-from py_unsio import *
+from unsio import *
 from uns_simu import *
 
 import argparse

py/mains/sim_mass.py

@@ -2,7 +2,7 @@
 
 from __future__ import print_function
 import sys
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import argparse
 
 

py/mains/stars_age.py

@@ -6,7 +6,7 @@
 # save stars particles born before/after a specific time
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/stream.py

@@ -2,7 +2,7 @@
 
 from __future__ import print_function
 import sys
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import argparse
 
 import time

py/mains/stretch.py

@@ -5,7 +5,7 @@ from __future__ import print_function
 # save stars particles to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/temp_to_density.py

@@ -6,7 +6,7 @@
 # save gas particles temperature to density field for displaying with glnemo2
 
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/mains/test_grid.py

+#!/usr/bin/env python
+from __future__ import print_function
+
+import numpy as np
+import os,time
+import sys
+import argparse,textwrap
+import scipy.ndimage as ndi
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# commandLine, parse the command line 
+def commandLine():
+
+    # help
+    parser = argparse.ArgumentParser(description="Test grid",
+                                    formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    parser.add_argument('--out', help="if blank display on screen, else on given file ",default="",type=str)
+    parser.add_argument('--sigma', help="gaussian sigma ",default=6.,type=float)
+    parser.add_argument('--noxz',help='no XZ projection',dest="noxz", action="store_true", default=False)
+    parser.add_argument('--contour',help='toggle contour display',dest="contour", action="store_true", default=False)
+    parser.add_argument('--cmap', help="color map (see mathplotlib colormap)",default="jet")
+    parser.add_argument('--verbose',help='verbose mode',dest="verbose", action="store_true", default=False)
+
+     # parse
+    args = parser.parse_args()
+
+    # start main funciton
+    process(args)
+
+# -----------------------------------------------------
+# process, is the core function
+def process(args):
+    # select matplotlib backend 
+    if args.out!= "": # non interactive
+        import matplotlib
+        matplotlib.use('Agg')
+
+    try:
+        fullProcess(out=args.out,sigma=args.sigma,cmap=args.cmap,noxz=args.noxz, contour=args.contour)
+    except Exception as x :
+        print (x.message,file=sys.stderr)
+    except KeyboardInterrupt:
+        sys.exit()
+
+
+#
+#
+#
+def fullProcess(out,sigma,noxz=False, contour=False, cmap="jet",ncols=3):
+    import matplotlib.colors
+    import matplotlib.pyplot as plt
+    import matplotlib.gridspec as gridspec
+        
+    t0=time.clock()
+    sigma_ori=sigma
+
+    # set up grid display
+    nrows=2
+    if noxz: # no XZ projection
+        nrows=1
+    ncols=ncols
+
+    # compute aspect ratio
+    mydpi=80
+
+    if nrows<ncols:
+        inches=19
+        #inches = 1920./mydpi # 1920
+        w=inches
+        h=inches*nrows/ncols
+    else: # nrows>ncols
+        inches = 1080./mydpi
+        w=inches*ncols/nrows
+        h=inches
+
+    print("w/h=",w,h,w*mydpi,h*mydpi)
+
+    # specify figure dimensions
+    fig=plt.figure(figsize=(w,h),dpi=mydpi)
+    #fig=plt.figure(figsize=(w,h))
+    print ("FIG DPI =",fig.dpi)
+    # create grid
+    gs = gridspec.GridSpec(nrows, ncols)#,wspace=0,hspace=0)#height_ratios=h,width_ratios=w)
+
+    for r in range(nrows):
+        for c in range(ncols):
+            ax = plt.subplot(gs[r, c])        
+            ax.set(aspect=1)
+            zz=np.random.random((102,102))
+            qq=ndi.gaussian_filter(zz,sigma=1.6,order=0)
+            im = ax.imshow(qq, norm = matplotlib.colors.LogNorm(), cmap=cmap)
+            plt.contour(qq,cmap="Paired")
+            ax.set_xticks([])
+            ax.set_yticks([])
+            if r != nrows-1:
+                ax.set_xticks([])
+            if  c!=0:
+                ax.set_yticks([])
+            ax.set_xticklabels("Hey")
+            fig.subplots_adjust(hspace=0.,wspace=0.)
+
+    fig.subplots_adjust(hspace=0.,wspace=0.)
+    print("Overall time [%.3f] sec"%(time.clock()-t0),file=sys.stderr)
+    if (out==''):
+        plt.show()
+    else:
+        outfile=out
+        print (">> ",outfile)
+        plt.savefig(outfile, bbox_inches=0,dpi=fig.dpi)
+    plt.close(fig)
+
+
+# -----------------------------------------------------
+# main program
+if __name__ == '__main__':
+  commandLine()
+
+

py/mains/test_unsio.py

@@ -5,8 +5,8 @@ import sys
 sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
 
 #from py_unstools import *         # import py_unstools package
-from py_unsio import *
-from uns_simu import *
+#from unsio import *
+#from uns_simu import *
 
 import argparse
 import os

py/mains/uns_cod.py

@@ -5,6 +5,7 @@ from uns_simu import *
 from simulations.ccod import * 
 import argparse
 
+sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # commandLine, parse the command line 
@@ -14,7 +15,7 @@ def commandLine():
     fastcod=True
     threshold=10000
      # help
-    parser = argparse.ArgumentParser(description="Convert enzo simulation to gdget2",
+    parser = argparse.ArgumentParser(description="Compute COD on simulation",
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     # options
     parser.add_argument('simname', help='Simulation name')

py/mains/uns_extract_halo.py

+#!/usr/bin/env python
+
+import sys
+from uns_simu import *
+from simulations.ccod import * 
+import argparse
+
+sys.path=['/home/jcl/works/GIT/uns_projects/py/modules/','/home/jcl/works/GIT/uns_projects/py/modules/simulations']+sys.path
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# commandLine, parse the command line 
+def commandLine():
+    dbname=None
+    ncores=None
+    fastcod=True
+    threshold=10000
+     # help
+    parser = argparse.ArgumentParser(description="Extract halo from multiple MDF halo simulation",
+                                    formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # options
+    parser.add_argument('simname', help='Simulation name')
+    parser.add_argument('haloN', help='Selected component')
+    parser.add_argument('--dbname',help='UNS database file name', default=dbname)
+    parser.add_argument('--verbose',help='verbose mode', default=False)
+
+     # parse
+    args = parser.parse_args()
+
+    # start main funciton
+    process(args)
+
+
+# -----------------------------------------------------
+# process, is the core function
+def process(args):
+    
+    pass
+    
+
+# -----------------------------------------------------
+# main program
+if __name__ == '__main__':
+    commandLine()

py/mains/uns_glindex_select.py

@@ -16,8 +16,8 @@
 from __future__ import print_function
 # unsio module loading
 # ==> do not forget to update PYTHONPATH environment variable with
-#     py_unsio location path
-from py_unsio import *
+#     unsio location path
+from unsio import *
 
 import numpy as np
 # cmd line

py/mains/uns_mult4sym.py

 # unsio
-from py_unsio import *
+from unsio import *
 import numpy as np
 # cnd line
 import sys, getopt

py/mains/uns_select_byid.py

@@ -2,7 +2,7 @@
 
 from __future__ import print_function
 import sys
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np
 import argparse
 #from IPython import embed

py/mains/velocity_to_density.py

@@ -7,7 +7,7 @@
 
 from __future__ import print_function
 # MANDATORY
-from py_unsio import *            # import py_unsio package (UNSIO)
+from unsio import *            # import unsio package (UNSIO)
 import numpy as np                # arrays are treated as numpy arrays
 import math
 import argparse

py/modules/simulations/ccod.py

-#!/usr/bin/python
+#!/usr/bin/env python
 from __future__ import print_function
 import sys
 from uns_simu import *
@@ -8,7 +8,12 @@ from ctree import *
 
 from multiprocessing import Process, Lock,Pool
 import multiprocessing
-import Queue # necessary to raise Queue.Empty signal
+is_py2 = sys.version[0] == '2'
+if is_py2:
+    import Queue as Queue
+else:
+    import queue as Queue
+#import Queue # necessary to raise Queue.Empty signal
 import time
 import os
 import signal
@@ -41,7 +46,7 @@ class CCod:
     # ----
     #
     # constructor
-    def __init__(self,simname,analysis=None,cod_dir_name=None,dbname=None,verbose=False,verbose_debug=False):
+    def __init__(self,simname,analysis=None,cod_dir_name=None,cod_base=None,dbname=None,threshold=None,verbose=False,verbose_debug=False):
         """
         simname must be a UNS simulation belonging to a uns sqlite3 database.
         infos regarding to simname simulation are loaded into privates variables
@@ -49,6 +54,9 @@ class CCod:
         self.__vdebug=verbose_debug
         self.__verbose=verbose
 
+        if threshold is not None:
+            self.__ctree_threshold =threshold
+            
         if cod_dir_name is not None:
             self.__COD_DIR_NAME=cod_dir_name
 

py/modules/simulations/csnapshot.py

@@ -2,7 +2,7 @@
 from __future__ import print_function
 
 #from py_unstools import *         # import py_unstools package
-from py_unsio import *
+import unsio
 from uns_simu import *
 from cfalcon import *
 from ccod import *
@@ -37,11 +37,11 @@ class CSnapshot:
             if float32:
                 if self.__vdebug:
                     print("32 bits",simname,select,times,verbose,type(simname),type(select))
-                self.__uns=CunsIn(simname,select,times,verbose)
+                self.__uns=unsio.CunsIn(simname,select,times,verbose)
             else:
                 if self.__vdebug:
                     print("64 bits",simname,select,times,verbose)
-                self.__uns=CunsInD(simname,select,times,verbose)
+                self.__uns=unsio.CunsInD(simname,select,times,verbose)
             if not self.__uns.isValid():
                 raise RuntimeError("UNS not valid")
         else:

py/modules/simulations/ctestunsio.py

 #!/usr/bin/env python
 from __future__ import print_function
 
-from uns_simu import *
+#from uns_simu import *
 import os,sys
 import numpy as np
 import tempfile
 
-import py_unsio as unsio
+import unsio as unsio
 from csnapshot import *
 
 import subprocess
@@ -211,4 +211,34 @@ class CTestunsio:
             self.__compareModel(unstype=mm,single=self.__single)