Some features in OpenFoamSimu class (#62)

* Modify openfoamsimu to account for the new name file format in sedfoam

* Remove the automatic use of find_directory function

* Modify path and file definition in openfoamsimu class

* Add possibility to load local directory simulation in OpenFoamSimu

* In openfoamsimu, add dataToLoad option to load only desired variables.

---------

Authored-by: Remi.Chassagne <remi.chassagne@legi.grenoble-inp.fr>

Author: remichassagne

fluidfoam/openfoamsimu.py

@@ -11,7 +11,8 @@
 
 import os, sys
 import subprocess
-from fluidfoam import readmesh, readfield
+import numpy as np
+from fluidfoam import readmesh, readfield, OpenFoamFile
 
 class Error(Exception):
     pass
@@ -34,21 +35,56 @@ class OpenFoamSimu(object):
             If simu=None, it will lists all existing simulation names in path
             and ask you to choose.\n
         timeStep: str, timeStep to load. If None, load the last time step\n
-        structured: bool, true if the mesh is structured
+        structured: bool, true if the mesh is structured\n
+        dataToLoad: list of str, list containing the name of the varaibles 
+            to read and load. If None, read and load all saved variables.
     """
 
-    def __init__(self, path, simu=None, timeStep=None, structured=False):
-
-        if simu == None:
+    def __init__(self, path=None, simu=None, timeStep=None, structured=False,
+                dataToLoad=None, precision=10, order='F'):
+        
+        if path == None and simu == None:
+            # If nothing if given, consider the current directory as the 
+            # simulation to load
+            self.directory = os.getcwd()+'/'
+            self.simu = os.getcwd().split('/')[-1]
+        elif simu == None:
+            # If only path is provided, consider all subfolders as possible
+            # simulations to load
             self.directory = self._choose_simulation(path)
             self.simu = self.directory.split("/")[-2]
         else:
+            # If path and simu are provided, consider the given directory
+            # as the simulation to load
             self.simu = simu
-            self.directory = self._find_directory(path, simu)
-
-        self.readopenfoam(timeStep=timeStep, structured=structured)
-
-    def readopenfoam(self, timeStep=None, structured=True):
+            if path.endswith('/') is False:
+                path += '/'
+            self.directory = path + simu
+            if self.directory.endswith('/') is False: 
+                self.directory += '/'
+
+        self.readmesh(structured=structured, precision=precision,
+                      order=order)
+        self.readopenfoam(timeStep=timeStep, structured=structured, 
+                          dataToLoad=dataToLoad, precision=precision,
+                          order=order)
+
+    def readmesh(self, structured=False, precision=10, order='F'):
+
+        X, Y, Z = readmesh(self.directory, structured=structured,
+                           precision=precision, order=order)
+        self.x = X
+        self.y = Y
+        self.z = Z
+        if structured:
+            nx = np.unique(X).size
+            ny = np.unique(Y).size
+            nz = np.unique(Z).size
+            self.ind = np.array(range(nx*ny*nz))
+            self.shape = (nx, ny, nz)
+
+    def readopenfoam(self, timeStep=None, structured=False, dataToLoad=None,
+                     precision=10, order='F'):
         """
         Reading SedFoam results
         Load the last time step saved of the simulation
@@ -57,6 +93,7 @@ def readopenfoam(self, timeStep=None, structured=True):
             timeStep : str or int, timeStep to load. If None, load the last time step\n
             structured : bool, true if the mesh is structured
         """
+
         if timeStep is None:
             dir_list = os.listdir(self.directory)
             time_list = []
@@ -76,29 +113,73 @@ def readopenfoam(self, timeStep=None, structured=True):
 
         self.timeStep = timeStep
 
-        #Read Mesh
-        X, Y, Z = readmesh(self.directory, structured=structured)
-        self.x = X
-        self.y = Y
-        self.z = Z
-
         #List all variables saved at the required time step removing potential
         #directory that cannot be loaded
-        self.variables = []
-        basepath = self.directory+self.timeStep+'/'
-        for fname in os.listdir(basepath):
-            path = os.path.join(basepath, fname)
-            if os.path.isdir(path):
-                # skip directories
-                continue
-            else:
-                self.variables.append(fname)
-
+        if dataToLoad is None:
+            self.variables = []
+            basepath = self.directory+self.timeStep+'/'
+            for fname in os.listdir(basepath):
+                path = os.path.join(basepath, fname)
+                if os.path.isdir(path):
+                    # skip directories
+                    continue
+                else:
+                    self.variables.append(fname)
+        else:
+            self.variables = dataToLoad
 
         for var in self.variables:
             #Load all variables and assign them as a variable of the object
-            self.__setattr__(var, readfield(path=self.directory,
-                time_name=self.timeStep, name=var, structured=structured))
+            field = OpenFoamFile(path=self.directory, time_name=self.timeStep,
+                                 name = var, structured=False, precision=precision,
+                                 order=order)
+            values = field.values
+
+            if field.type_data == "scalar":
+                if structured and not field.uniform:
+                    try:
+                        values = np.reshape(values[self.ind], self.shape, order=order)
+                    except:
+                        print("Variable {} could not be loaded".format(var))
+                        self.variables.remove(var)
+                        continue
+            elif field.type_data == "vector":
+                shape = (3, values.size // 3)
+                values = np.reshape(values, shape, order=order)
+                if structured and not field.uniform:
+                    try:
+                        values[0:3, :] = values[0:3, self.ind]
+                        shape = (3,) + tuple(self.shape)
+                        values = np.reshape(values, shape, order=order)
+                    except:
+                        print("Variable {} could not be loaded".format(var))
+                        self.variables.remove(var)
+                        continue
+            elif field.type_data == "symmtensor":
+                shape = (6, values.size // 6)
+                values = np.reshape(values, shape, order=order)
+                if structured and not field.uniform:
+                    try:
+                        values[0:6, :] = values[0:6, self.ind]
+                        shape = (6,) + tuple(self.shape)
+                        values = np.reshape(values, shape, order=order)
+                    except:
+                        print("Variable {} could not be loaded".format(var))
+                        self.variables.remove(var)
+                        continue
+            elif field.type_data == "tensor":
+                shape = (9, values.size // 9)
+                values = np.reshape(values, shape, order=order)
+                if structured and not field.uniform:
+                    try:
+                        values[0:9, :] = values[0:9, self.ind]
+                        shape = (9,) + tuple(self.shape)
+                        values = np.reshape(values, shape, order=order)
+                    except:
+                        print("Variable {} could not be loaded".format(var))
+                        self.variables.remove(var)
+                        continue
+            self.__setattr__(var.replace('.', '_'), values)
 
     def keys(self):
         """

fluidfoam/test_openfoamsimu.py

@@ -9,6 +9,6 @@
 
 class SimpleTestCase(unittest.TestCase):
     def test_read_simu(self):
-        mySimu = OpenFoamSimu(path=case, simu=simu, timeStep=timeStep, structured=True)
+        mySimu = OpenFoamSimu(path=case, simu=simu, timeStep=timeStep, structured=True, precision=12)
         keys = mySimu.keys()
-        self.assertEqual(np.mean(mySimu.U), 0.03630165464270426)
+        self.assertEqual(np.mean(mySimu.U), 0.036301654642704254)