Index: wflow-py/Scripts/bmi2runner.py
===================================================================
diff -u -r42fd01a5e3fcb6d0fa9f8f9880c74cd282dc0d0f -rdbb856e2a6f375e5c7f2db502d7ca90b9fbcf421
--- wflow-py/Scripts/bmi2runner.py	(.../bmi2runner.py)	(revision 42fd01a5e3fcb6d0fa9f8f9880c74cd282dc0d0f)
+++ wflow-py/Scripts/bmi2runner.py	(.../bmi2runner.py)	(revision dbb856e2a6f375e5c7f2db502d7ca90b9fbcf421)
@@ -71,7 +71,6 @@
     end = bmiobj.get_end_time()
     ts = bmiobj.get_time_step()
     curtime = bmiobj.get_current_time()
-
     # Loop over the time duration
     while curtime < end:
         bmiobj.update_until(curtime + ts)
Index: wflow-py/wflow/wf_DynamicFramework.py
===================================================================
diff -u -r8e62145254bea78f01d01e69573753ba631ecef5 -rdbb856e2a6f375e5c7f2db502d7ca90b9fbcf421
--- wflow-py/wflow/wf_DynamicFramework.py	(.../wf_DynamicFramework.py)	(revision 8e62145254bea78f01d01e69573753ba631ecef5)
+++ wflow-py/wflow/wf_DynamicFramework.py	(.../wf_DynamicFramework.py)	(revision dbb856e2a6f375e5c7f2db502d7ca90b9fbcf421)
@@ -547,13 +547,6 @@
         """
         Makes sure the logging closed
         """
-        try:
-            pcrut.logging.shutdown()
-            for ofile_list in self.oscv:
-                self.oscv[ofile_list].closeall()
-        except:
-            return
-
         if hasattr(self, 'NcOutput'):
             self.NcOutput.finish()
 
@@ -1241,7 +1234,7 @@
         :returns: 1 if the map was present, 0 if a new map was created
         """
 
-        arpcr = numpy2pcr(Scalar, values.copy(), -999)
+        arpcr = numpy2pcr(Scalar, flipud(values).copy(), -999)
 
         self.setviaAPI[mapname] = 1
 
@@ -1520,7 +1513,7 @@
     def wf_supplyMapAsNumpy(self, mapname):
         """
         Returns a numpy array (matrix) for the specified map and the current
-        timestep. If the maps is not dynamic the current staus of the map is
+        timestep. If the maps is not dynamic the current status of the map is
         returns which may be undefined for maps that are filled with data
         at the end of a run
         Missing value is -999
@@ -1535,7 +1528,8 @@
             # exec "retval = pcr2numpy(self._userModel()." + mapname + ",-999)"
             pcrmap = getattr(self._userModel(), mapname)
             if isinstance(pcrmap, pcraster._pcraster.Field):
-                retval = pcr_as_numpy(pcrmap)
+                tt = pcr2numpy(pcrmap,-999.0)
+                retval = flipud(tt).copy()
             else:
                 retval = pcrmap
             if self.APIDebug:
@@ -1555,9 +1549,9 @@
         """
 
         x = xcoordinate((spatial(boolean(1.0))))
-        retval = pcr_as_numpy(x)
+        retval = pcr_as_numpy(x).copy()
 
-        return retval
+        return flipud(retval).copy()
 
     def wf_supplyMapYAsNumpy(self):
         """
@@ -1568,9 +1562,9 @@
         """
 
         y = ycoordinate((spatial(boolean(1.0))))
-        retval = pcr_as_numpy(y)
+        retval = pcr_as_numpy(y).copy()
 
-        return retval
+        return flipud(retval).copy()
 
     def wf_supplyMapZAsNumpy(self):
         """
@@ -1584,7 +1578,7 @@
         if hasattr(self._userModel(), 'Altitude'):
             retval = getattr(self._userModel(), 'Altitude')
 
-            return pcr2numpy(retval, -999)
+            return flipud(pcr2numpy(retval, -999)).copy()
         else:
             self.logger.warn("Altitude is not defined in the usermodel, returning empty list")
             return []
Index: wflow-py/wflow/wflow_bmi.py
===================================================================
diff -u -r42fd01a5e3fcb6d0fa9f8f9880c74cd282dc0d0f -rdbb856e2a6f375e5c7f2db502d7ca90b9fbcf421
--- wflow-py/wflow/wflow_bmi.py	(.../wflow_bmi.py)	(revision 42fd01a5e3fcb6d0fa9f8f9880c74cd282dc0d0f)
+++ wflow-py/wflow/wflow_bmi.py	(.../wflow_bmi.py)	(revision dbb856e2a6f375e5c7f2db502d7ca90b9fbcf421)
@@ -9,6 +9,7 @@
 import wflow_lib
 import numpy as np
 from wflow.pcrut import setlogger
+from pcraster import *
 
 class wflowbmi_light(object):
     """
@@ -272,11 +273,11 @@
 
         if self.wrtodisk:
             fname = str(self.currenttimestep) + "_get_" + long_var_name + ".map"
-            arpcr = self.dynModel.numpy2pcr(self.dynModel.Scalar, src, -999)
+            arpcr = numpy2pcr(Scalar, src, -999)
             self.bmilogger.debug("Writing to disk: " + fname)
-            self.dynModel.report(arpcr,fname)
+            report(arpcr,fname)
 
-        return np.flipud(src)
+        return src
 
     def set_var(self, long_var_name, src):
         """
@@ -289,9 +290,9 @@
 
         if self.wrtodisk:
             fname = str(self.currenttimestep) + "_set_" + long_var_name + ".map"
-            arpcr = self.dynModel.numpy2pcr(self.dynModel.Scalar, np.flipud(src), -999)
+            arpcr = numpy2pcr(Scalar, src, -999)
             self.bmilogger.debug("Writing to disk: " + fname)
-            self.dynModel.report(arpcr,fname)
+            report(arpcr,fname)
 
         if long_var_name in self.outputonlyvars:
             self.bmilogger.error("set_var: " + long_var_name + " is listed as an output only variable, cannot set. " + str(self.outputonlyvars))
@@ -302,7 +303,7 @@
                 self.dynModel.wf_setValues(long_var_name,float(src))
             else:
                 self.bmilogger.debug("set_var: (grid) " + long_var_name)
-                self.dynModel.wf_setValuesAsNumpy(long_var_name, np.flipud(src))
+                self.dynModel.wf_setValuesAsNumpy(long_var_name, src)
 
 
     def set_var_slice(self, name, start, count, var):
@@ -314,7 +315,7 @@
         For some implementations it can be equivalent and more efficient to do:
         `get_var(name)[start[0]:start[0]+count[0], ..., start[n]:start[n]+count[n]] = var`
         """
-        tmp = np.flipud(self.get_var(name).copy())
+        tmp = self.get_var(name).copy()
         try:
             # if we have start and count as a number we can do this
             tmp[start:(start+count)] = var
@@ -323,7 +324,7 @@
             slices = [np.s_[i:(i+n)] for i,n in zip(start, count)]
             tmp[slices]
 
-        self.set_var(name, name, np.flipud(tmp))
+        self.set_var(name, name, tmp)
 
     def set_var_index(self, name, index, var):
         """
@@ -335,9 +336,9 @@
         and more efficient to do:
         `get_var(name).flat[index] = var`
         """
-        tmp = np.flipud(self.get_var(name).copy())
+        tmp = self.get_var(name).copy()
         tmp.flat[index] = var
-        self.set_var(name, name, np.flipud(tmp))
+        self.set_var(name, name, tmp)
 
     def inq_compound(self, name):
         """
@@ -394,7 +395,7 @@
         logstr = os.getenv('wflow_bmi_loglevel', 'ERROR')
         self.wrtodisk = False
 
-        if os.getenv("wflow_bmi_writedisk",'False') in 'True':
+        if os.getenv("wflow_bmi_writetodisk",'False') in 'True':
             self.wrtodisk = True
 
         if logstr in 'ERROR':
@@ -408,6 +409,8 @@
 
         self.bmilogger = setlogger('wflow_bmi.log','wflow_bmi_logging',thelevel=self.loggingmode)
         self.bmilogger.info("__init__: wflow_bmi object initialised.")
+        if self.wrtodisk:
+            self.bmilogger.warn('Will write all bmi set and get grids to disk!...')
 
 
     def initialize_config(self, filename, loglevel=logging.DEBUG):
@@ -836,17 +839,14 @@
         if long_var_name in self.inputoutputvars:
             ret = self.dynModel.wf_supplyMapAsNumpy(long_var_name)
             self.bmilogger.debug("get_value: " + long_var_name)
+
             if self.wrtodisk:
                 fname = str(self.currenttimestep) + "_get_" + long_var_name + ".map"
-                arpcr = self.dynModel.numpy2pcr(self.dynModel.Scalar, ret, -999)
+                arpcr = numpy2pcr(Scalar, ret, -999)
                 self.bmilogger.debug("Writing to disk: " + fname)
-                self.dynModel.report(arpcr,fname)
+                report(arpcr,fname)
 
-            try:
-                fret = np.flipud(ret)
-                return fret
-            except:
-                return ret
+            return ret
         else:
             self.bmilogger.error("get_value: " + long_var_name + ' not in list of output values ' + str(self.inputoutputvars))
             return None
@@ -863,7 +863,7 @@
 
         if long_var_name in self.inputoutputvars:
             self.bmilogger.debug("get_value_at_indices: " + long_var_name + ' at ' + str(inds))
-            npmap = np.flipud(self.dynModel.wf_supplyMapAsNumpy(long_var_name))
+            npmap = self.dynModel.wf_supplyMapAsNumpy(long_var_name)
             return npmap[inds]
         else:
             self.bmilogger.error("get_value_at_indices: " + long_var_name + ' not in list of output values ' + str(self.inputoutputvars))
@@ -886,9 +886,9 @@
             raise ValueError("set_value_at_indices: " + long_var_name + " is listed as an output only variable, cannot set. " + str(self.outputonlyvars))
         else:
             self.bmilogger.debug("set_value_at_indices: " + long_var_name + ' at ' + str(inds))
-            npmap = np.flipud(self.dynModel.wf_supplyMapAsNumpy(long_var_name))
+            npmap = self.dynModel.wf_supplyMapAsNumpy(long_var_name)
             npmap[inds] = src
-            self.dynModel.wf_setValuesAsNumpy(long_var_name,np.flipud(npmap))
+            self.dynModel.wf_setValuesAsNumpy(long_var_name,npmap)
 
     def get_grid_type(self, long_var_name):
         """
@@ -970,7 +970,7 @@
 
         """
         self.bmilogger.debug("get_grid_y: " + long_var_name)
-        return np.flipud(self.dynModel.wf_supplyMapYAsNumpy())
+        return self.dynModel.wf_supplyMapYAsNumpy()
 
     def get_grid_z(self, long_var_name):
         """
@@ -981,7 +981,7 @@
         :return: Numpy array of doubles: z coordinate of grid cell center for each grid cell, in the same order as the values returned by function get_value.
         """
         self.bmilogger.debug("get_grid_z: " + long_var_name)
-        return np.flipud(self.dynModel.wf_supplyMapZAsNumpy())
+        return self.dynModel.wf_supplyMapZAsNumpy()
 
     def get_var_units(self, long_var_name):
         """
@@ -1016,9 +1016,9 @@
         self.bmilogger.debug("set_value: " + long_var_name + ":" + str(src))
         if self.wrtodisk:
             fname = str(self.currenttimestep) + "_set_" + long_var_name + ".map"
-            arpcr = self.dynModel.numpy2pcr(self.dynModel.Scalar, src, -999)
+            arpcr = numpy2pcr(Scalar, src, -999)
             self.bmilogger.debug("Writing to disk: " + fname)
-            self.dynModel.report(arpcr,fname)
+            report(arpcr,fname)
 
         if long_var_name in self.outputonlyvars:
             self.bmilogger.error("set_value: " + long_var_name + " is listed as an output only variable, cannot set. " + str(self.outputonlyvars))
@@ -1029,7 +1029,7 @@
                 self.dynModel.wf_setValues(long_var_name,float(src))
             else:
                 self.bmilogger.debug("set_value: (grid) " + long_var_name)
-                self.dynModel.wf_setValuesAsNumpy(long_var_name, np.flipud(src))
+                self.dynModel.wf_setValuesAsNumpy(long_var_name, src)
 
     def get_grid_connectivity(self, long_var_name):
         """
Index: wflow-py/wflow/wflow_bmi_combined.py
===================================================================
diff -u -r8e62145254bea78f01d01e69573753ba631ecef5 -rdbb856e2a6f375e5c7f2db502d7ca90b9fbcf421
--- wflow-py/wflow/wflow_bmi_combined.py	(.../wflow_bmi_combined.py)	(revision 8e62145254bea78f01d01e69573753ba631ecef5)
+++ wflow-py/wflow/wflow_bmi_combined.py	(.../wflow_bmi_combined.py)	(revision dbb856e2a6f375e5c7f2db502d7ca90b9fbcf421)
@@ -6,8 +6,9 @@
 from wflow.pcrut import setlogger
 from wflow.wflow_lib import configget
 import ConfigParser
+import logging
+from pcraster import *
 
-
 def iniFileSetUp(configfile):
     """
     Reads .ini file and returns a config object.
@@ -60,7 +61,28 @@
         self.currenttimestep = 0
         self.exchanges = []
         self.comp_sep = "@"
+        self.wrtodisk = False
+        if os.getenv("wflow_bmi_writetodisk",'False') in 'True':
+            self.wrtodisk = True
 
+        self.loggingmode = logging.ERROR
+        logstr = os.getenv('wflow_bmi_loglevel', 'ERROR')
+        if logstr in 'ERROR':
+            self.loggingmode = logging.ERROR
+        if logstr in 'WARNING':
+            self.loggingmode = logging.WARNING
+        if logstr in 'INFO':
+            self.loggingmode = logging.INFO
+        if logstr in 'DEBUG':
+            self.loggingmode = logging.DEBUG
+
+        self.bmilogger = setlogger('wflow_bmi_combined.log','wflow_bmi_combined_logging',thelevel=self.loggingmode)
+        self.bmilogger.info("__init__: wflow_bmi_combined object initialised.")
+        if self.wrtodisk:
+            self.bmilogger.warn('Will write all bmi set and get grids to disk!...')
+
+
+
     def __getmodulenamefromvar__(self,long_var_name):
         """
 
@@ -209,7 +231,7 @@
             for item in self.exchanges:
                 supplymodel = self.__getmodulenamefromvar__(item)
                 if curmodel == supplymodel:
-                    outofmodel = self.get_value(item).copy()
+                    outofmodel = self.get_value(item)
                     tomodel = self.config.get('exchanges',item)
                     self.set_value(tomodel,outofmodel)
 
@@ -285,6 +307,8 @@
         for key, value in self.bmimodels.iteritems():
             self.bmimodels[key].finalize()
 
+        self.bmilogger.info("finalize.")
+
     def get_component_name(self):
         """
         :return:  identifier of the models separated by a comma (,)
@@ -436,7 +460,7 @@
         for key, value in self.bmimodels.iteritems():
             st.append(self.bmimodels[key].get_time_step())
 
-        return max(st)
+        return max(st)[0]
 
     def get_time_units(self):
         """
@@ -461,10 +485,15 @@
         :return: a np array of long_var_name
         """
         # first part should be the component name
+        self.bmilogger.debug('get_value: ' + long_var_name)
         cname = long_var_name.split(self.comp_sep)
         if self.bmimodels.has_key(cname[0]):
-            return self.bmimodels[cname[0]].get_value(cname[1])
+            tmp = self.bmimodels[cname[0]].get_value(cname[1])
+            if self.wrtodisk:
+                report(numpy2pcr(Scalar,tmp, -999),long_var_name + "_get_" + str(self.get_current_time()) + '.map')
+            return tmp
         else:
+            self.bmilogger.error('get_value: ' + long_var_name + ' returning None!!!!')
             return None
 
 
@@ -639,12 +668,16 @@
                   is present a uniform map will be set in the wflow model.
         """
         # first part should be the component name
+        self.bmilogger.debug('set_value: ' + long_var_name)
         cname = long_var_name.split(self.comp_sep)
         if self.bmimodels.has_key(cname[0]):
             self.bmimodels[cname[0]].set_value(cname[1],src)
+            if self.wrtodisk:
+                report(numpy2pcr(Scalar,src, -999),long_var_name + "_set_" + str(self.get_current_time()) + '.map')
 
 
 
+
     def get_grid_connectivity(self, long_var_name):
         """
         Not applicable, raises NotImplementedError