[fix] be sure to start the external programs in the right directory

pylot/core/active/fmtomoUtils.py

@@ -49,7 +49,8 @@ class Tomo3d(object):
             os.system('ln -s %s %s'%(filename, linkname))
 
     def buildObsdata(self):
-        os.system('obsdata')
+        p = subprocess.Popen(os.path.join(self.cwd, 'obsdata'), shell=True)
+        os.waitpid(p.pid)
         os.system('mv sources.in sourcesref.in')
 
     def defFMMParas(self):
@@ -57,9 +58,9 @@ class Tomo3d(object):
         Initiates parameters for the forward calculation.
         '''
         # Name of fast marching program
-        self.fmm = '{0}/fm3d'.format(self.cwd)
+        self.fmm = os.path.join(self.cwd, 'fm3d')
         # Name of program calculating Frechet derivatives
-        self.frechgen = '{0}/frechgen'.format(self.cwd)
+        self.frechgen = os.path.join(self.cwd, 'frechgen')
         # Name of current velocity/inversion grid
         self.cvg = 'vgrids.in'
         # Name of current interfaces grid
@@ -116,7 +117,7 @@ class Tomo3d(object):
         Default: pwd
         '''
         if directory == None:
-            directory = os.path.join(os.getcwd(), self.simuldir)
+            directory = self.simuldir
 
         os.chdir(directory)
         self.cwd = directory