Added Astaroth 2.0

analysis/python/astar/data/__init__.py

@@ -0,0 +1,21 @@
+'''
+    Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
+
+    This file is part of Astaroth.
+
+    Astaroth is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Astaroth is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Astaroth.  If not, see <http://www.gnu.org/licenses/>.
+'''
+
+
+from . import read

analysis/python/astar/data/read.py

@@ -0,0 +1,142 @@
+'''
+    Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
+
+    This file is part of Astaroth.
+
+    Astaroth is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Astaroth is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Astaroth.  If not, see <http://www.gnu.org/licenses/>.
+'''
+
+# This module is for reading data.
+
+import numpy as np
+
+def read_bin(fname, fdir, fnum, minfo, numtype=np.longdouble):
+    '''Read in a floating point array'''
+    filename = fdir + fname + '_' + fnum + '.mesh'
+    datas = np.DataSource()
+    read_ok = datas.exists(filename)
+    if read_ok:
+        print(filename)
+        array = np.fromfile(filename, dtype=numtype)
+
+        timestamp = array[0]
+
+        array = np.reshape(array[1:], (minfo.contents['AC_mx'], 
+                                   minfo.contents['AC_my'], 
+                                   minfo.contents['AC_mz']), order='F')
+    else:
+        array = None
+        timestamp = None
+     
+    return array, timestamp, read_ok 
+
+def read_meshtxt(fdir, fname):
+    with open(fdir+fname) as f:
+        filetext = f.read().splitlines()
+
+    contents = {}  
+
+    for line in filetext:
+        line = line.split()
+        if line[0] == 'int':
+            contents[line[1]] = np.int(line[2])
+        elif line[0] == 'real':
+            contents[line[1]] = np.float(line[2])
+        else: 
+            print('ERROR: ' + line[0] +' no recognized!')
+
+    return contents
+
+class MeshInfo():
+    '''Object that contains all mesh info'''
+
+    def __init__(self, fdir):
+        self.contents = read_meshtxt(fdir, 'mesh_info.list') 
+
+class Mesh:
+    '''Class tha contains all 3d mesh data'''
+
+    def __init__(self, fnum, fdir=""):
+        fnum = str(fnum)
+        self.framenum = fnum.zfill(10)
+
+        self.minfo = MeshInfo(fdir)
+
+        self.lnrho, self.timestamp, self.ok = read_bin('VTXBUF_LNRHO', fdir, fnum, self.minfo)
+
+        if self.ok:
+
+            self.ss, timestamp, ok = read_bin('VTXBUF_ENTROPY', fdir, fnum, self.minfo)
+ 
+            #TODO Generalize is a dict. Do not hardcode!  
+            uux, timestamp, ok = read_bin('VTXBUF_UUX', fdir, fnum, self.minfo)
+            uuy, timestamp, ok = read_bin('VTXBUF_UUY', fdir, fnum, self.minfo) 
+            uuz, timestamp, ok = read_bin('VTXBUF_UUZ', fdir, fnum, self.minfo)
+            self.uu = (uux, uuy, uuz)
+            uux = []
+            uuy = [] 
+            uuz = []
+ 
+            aax, timestamp, ok = read_bin('VTXBUF_AX', fdir, fnum, self.minfo)
+            aay, timestamp, ok = read_bin('VTXBUF_AY', fdir, fnum, self.minfo) 
+            aaz, timestamp, ok = read_bin('VTXBUF_AZ', fdir, fnum, self.minfo)
+            self.aa = (aax, aay, aaz)
+            aax = []
+            aay = [] 
+            aaz = []
+
+            self.xx =  self.minfo.contents['AC_inv_dsx']*np.arange(self.minfo.contents['AC_mx'])
+            self.yy =  self.minfo.contents['AC_inv_dsy']*np.arange(self.minfo.contents['AC_my'])
+            self.zz =  self.minfo.contents['AC_inv_dsz']*np.arange(self.minfo.contents['AC_mz'])
+
+            self.xmid = int(self.minfo.contents['AC_mx']/2)
+            self.ymid = int(self.minfo.contents['AC_my']/2)
+            self.zmid = int(self.minfo.contents['AC_mz']/2)
+
+
+def parse_ts(fdir, fname):
+    with open(fdir+fname) as f:
+        filetext = f.read().splitlines()
+
+    var = {}  
+
+    line = filetext[0].split()
+    for i in range(len(line)):
+        line[i] = line[i].replace('VTXBUF_', "")
+        line[i] = line[i].replace('UU', "uu")
+        line[i] = line[i].replace('_total', "tot")
+        line[i] = line[i].replace('A', "aa")
+        line[i] = line[i].replace('LNRHO', "lnrho")
+        line[i] = line[i].replace('X', "x")
+        line[i] = line[i].replace('Y', "y")
+        line[i] = line[i].replace('Z', "z")
+
+    tsdata = np.loadtxt(fdir+fname,skiprows=1)
+
+    for i in range(len(line)):
+        var[line[i]] = tsdata[:,i]
+
+    var['step'] = np.int64(var['step'])
+
+    print("HERE ARE ALL KEYS FOR TS DATA:")
+    print(var.keys())
+   
+    return var
+
+class TimeSeries:
+    '''Class for time series data'''
+
+    def __init__(self, fdir="", fname="timeseries.ts"):
+
+        self.var = parse_ts(fdir, fname)