added pfg tests; reworked test handling; fixed some bugs

python/parfield/dorie/parfield/converter/base.py

@@ -42,6 +42,7 @@ class BaseConverter(object):
         out_path = self.read_parameter('general','outputFile')
         overwrite = text_to_bool(self.read_parameter('general','overwrite'))
         millerSimilarity = text_to_bool(self.read_parameter('generator','millerSimilarity'))
+        self.dim = int(self.read_parameter('generator','dimensions'))
 
         self.data_dict = self.read_data(input_file,millerSimilarity)
         self.write(out_path,overwrite)
@@ -58,6 +59,10 @@ class BaseConverter(object):
         if not self.data_dict:
             raise RuntimeError("Encountered empty data array (call read_data first)")
 
+        for v in self.data_dict.values():
+            if v.ndim != self.dim:
+                print(v.shape, self.dim)
+                raise ValueError("Data does not match field dimensions")
         h5_attrs = self._get_attributes()
         groupname = self.ParClass.classname
         write_parameter_file(groupname, self.data_dict, out_path,
@@ -87,9 +92,12 @@ class BaseConverter(object):
             raise RuntimeError("Missing option {}.{} in parameter file".format(section,key))
 
     def _get_attributes(self):
-        attr_dict = {
+        extensions = np.array(self.read_parameter("generator","extensions").split(), dtype=np.float64)
+        if not extensions.size == self.dim:
+            raise ValueError("Extensions do not match field dimensions")
+        attr = {
                 "millerSimilarity": np.bool(text_to_bool(self.read_parameter('generator','millerSimilarity'))),
                 "variance": np.float64(self.read_parameter("generator","variance")),
-                "extensions": np.array(self.read_parameter("generator","extensions").split(), dtype=np.float64)
+                "extensions": extensions
             }
-        return attr_dict
+        return attr

python/parfield/dorie/parfield/converter/h5.py

@@ -39,21 +39,25 @@ class H5Converter(BaseConverter):
             if "/rawField" in f:
                 raw_array = np.array(f.get("/rawField"), dtype=np.float64)
             else:
-                raw_array = np.zeros_like(media_array, dtype=np.float64)
+                raw_array = np.zeros_like(media_array)
 
         # check how many different media we are dealing with
         uq_media = np.sort(np.unique(media_array.astype(int)))
-        if uq_media != range(1,np.max(uq_media) + 1):
+        if not np.array_equal(uq_media,np.arange(1,np.max(uq_media) + 1)):
             raise IOError("Media numbering must be continuous, starting from 1")
-        p_dict = {i: self.create_parclass(i).parameters() for i in uq_media}
+        p = [self.create_parclass(i).parameters() for i in uq_media]
 
         # create parameter fields
         parField = {"raw_field": raw_array}
         for pn in self.ParClass.names:
-            parField[pn] = np.zeros_like(media_array, dtype=float)
+            parField[pn] = np.zeros_like(media_array)
             for i in uq_media:
-                mask = np.logical_and(media_array >= i, media_array < i + 1)
-                parField[pn][mask] = p[i][pn] * (media_array[mask] - i) \
-                                   + p[i+1][pn] * (i + 1 - media_array[mask])
+                mask = media_array == i
+                parField[pn][mask] = p[i-1][pn]
+
+                mask = np.logical_and(media_array > i, media_array < i + 1)
+                if np.any(mask):
+                    parField[pn][mask] = p[i-1][pn] * (media_array[mask] - i) \
+                                         + p[i][pn] * (i + 1 - media_array[mask])
 
         return parField

python/testtools/dorie/testtools/dorie_create/__init__.py

+from dorie.utilities._load_all_in_folder import load
+
+"""
+Import script to allow for statements of the form
+    from dorie.testtools.dorie_run import ode
+"""
+
+load("dorie.testtools.dorie_create",__file__)

python/testtools/dorie/testtools/dorie_create/compare.py

+import filecmp
+
+from dorie.testtools.utilities.decorators import evaluation_script
+
+@evaluation_script
+def evaluate(iniinfo,runtime):
+    fileset_1 = iniinfo["_compare.created_files"].split()
+    fileset_2 = iniinfo["_compare.reference_files"].split()
+    for f1,f2 in zip(fileset_1,fileset_2):
+        if not filecmp.cmp(f1,f2):
+            print("File contents of {} and {} do not match".format(f1,f2))
+            return False
+    return True

python/testtools/dorie/testtools/dorie_pfg/__init__.py

@@ -2,7 +2,7 @@ from dorie.utilities._load_all_in_folder import load
 
 """
 Import script to allow for statements of the form
-    from dorie.testtools.evaluation import ode
+    from dorie.testtools.dorie_pfg import correlation
 """
 
 load("dorie.testtools.dorie_pfg",__file__)

python/testtools/dorie/testtools/dorie_pfg/reference.py

+import os
+import h5py
+import numpy as np
+
+from dorie.testtools.utilities.decorators import evaluation_script
+from dorie.parfield.parameter_file import read_parameter_file
+
+
+@evaluation_script
+def evaluate(iniinfo,runtime):
+    outfile = iniinfo["general.outputFile"]
+    try:
+        reference = iniinfo["_reference.path"] + "/" + iniinfo["general.outputFile"]
+    except KeyError:
+        raise ValueError("The reference evaluator assumes the key _reference.path to be existent in the inifile")
+
+    if not os.path.isfile(reference):
+        raise RuntimeError("Reference file {} does not exist".format(reference))
+
+    f1_data, f1_attrs = read_parameter_file(outfile)
+    f2_data, f2_attrs = read_parameter_file(reference)
+
+    if f1_data.keys() != f2_data.keys() or f1_attrs.keys() != f2_attrs.keys():
+        print("Keys do not match")
+        return False
+
+    for key in f1_data.keys():
+        if not np.array_equal(f1_data[key],f2_data[key]):
+            print("Attributes do not match")
+            return False
+
+    for key in f1_data.keys():
+        if not np.array_equal(f1_data[key],f2_data[key]):
+            print("Data does not match in key {}".format(key))
+            return False
+
+    return True

python/testtools/dorie/testtools/dorie/__init__.py → python/testtools/dorie/testtools/dorie_run/__init__.py

@@ -2,7 +2,7 @@ from dorie.utilities._load_all_in_folder import load
 
 """
 Import script to allow for statements of the form
-    from dorie.testtools.evaluation import ode
+    from dorie.testtools.dorie_run import ode
 """
 
-load("dorie.testtools.dorie",__file__)
+load("dorie.testtools.dorie_run",__file__)

python/testtools/dorie/testtools/dorie/reference.py → python/testtools/dorie/testtools/dorie_run/reference.py

@@ -3,6 +3,7 @@ import os
 from dorie.testtools.utilities.decorators import evaluation_script
 from dorie.utilities.vtktools import pvd_reader
 from dorie.utilities.vtktools import vtkfile
+from dorie.utilities.text_to_bool import text_to_bool
 
 from dorie.utilities import fuzzy_compare_grid
 
@@ -14,16 +15,18 @@ def evaluate(iniinfo,runtime):
 
     try:
         reference = iniinfo["_reference.path"] + "/" + iniinfo["output.fileName"] + ".vtu"
-        if os.path.isfile(reference):
-            vtkfile_run = vtkfile.VTKFile(vtks[-1].path)
-            vtkfile_run.read()
-            vtkfile_ref = vtkfile.VTKFile(reference)
-            vtkfile_ref.read()
-            # demand equal grids when not using adaptivity
-            strict_compare = iniinfo["adaptivity.useAdaptivity"].lower() in ["false","0","off"]
-            ret = fuzzy_compare_grid.compare(vtkfile_run.grid, vtkfile_ref.grid, strict=strict_compare)
-        else:
-            raise RuntimeError("Reference file {} does not exist".format(reference))
     except KeyError:
         raise ValueError("The reference evaluator assumes the key _reference.path to be existent in the inifile")
+
+    if os.path.isfile(reference):
+        vtkfile_run = vtkfile.VTKFile(vtks[-1].path)
+        vtkfile_run.read()
+        vtkfile_ref = vtkfile.VTKFile(reference)
+        vtkfile_ref.read()
+        # demand equal grids when not using adaptivity
+        strict_compare = text_to_bool(iniinfo["adaptivity.useAdaptivity"])
+        ret = fuzzy_compare_grid.compare(vtkfile_run.grid, vtkfile_ref.grid, strict=strict_compare)
+    else:
+        raise RuntimeError("Reference file {} does not exist".format(reference))
+
     return ret

python/testtools/dorie/testtools/wrapper/test_dorie.py

@@ -3,18 +3,32 @@ import os
 import subprocess
 import inspect
 import time
-
-import dorie.testtools.dorie as evaluation
-
+import importlib
 
 def test_dorie(iniinfo,inifile,executable):
     """
-    Parses the parameter file, calls DORiE, calls the evaluation routines and exits with 0 (pass) or 1 (fail)
+    Parses the parameter file, calls DORiE, calls the evaluation routines and
+    exits with 0 (pass) or 1 (fail).
+
+    You can specify which command of the dorie wrapper to test with the `_test_command` key (e.g. `run`
+    for `dorie run`). Options to the dorie wrapper can be specified with `_test_command_options`.
+    The last argument given to the dorie wrapper is specified with `_test_target` (defaults to the ini file).
     """
     command = [executable]
-    if "__inifile_optionkey" in iniinfo:
-        command.append(iniinfo["__inifile_optionkey"])
-    command.append(inifile)
+    if not "_test_command" in iniinfo:
+        raise ValueError("Key _test_command has to be given")
+    test_command = iniinfo["_test_command"]
+    try:
+        evaluation = importlib.import_module("dorie.testtools.dorie_" + test_command)
+    except ImportError:
+        raise ValueError("Unknown test command " + test_command)
+    command.append(test_command)
+    if "_test_command_options" in iniinfo:
+        command.append(iniinfo["_test_command_options"])
+    if not "_test_target" in iniinfo:
+        command.append(inifile)
+    elif iniinfo["_test_target"] != "None":
+        command.append(iniinfo["_test_target"])
 
     # Run DORiE and measure total execution time
     start = time.clock()

python/testtools/dorie/testtools/wrapper/test_dorie_pfg.py

-import sys
-import os
-import subprocess
-import inspect
-import time
-
-import dorie.testtools.dorie_pfg as evaluation
-
-
-def test_dorie_pfg(iniinfo,inifile,executable):
-    """
-    Parses the parameter file, calls DORiE, calls the evaluation routines and exits with 0 (pass) or 1 (fail)
-    """
-    command = [executable]
-    if "__inifile_optionkey" in iniinfo:
-        command.append(iniinfo["__inifile_optionkey"])
-    command.append(inifile)
-
-    # Run DORiE and measure total execution time
-    start = time.clock()
-    return_code = subprocess.call(command)
-    end = time.clock()
-    runtime = end - start
-
-    if return_code != 0 or not "_evaluation" in iniinfo:
-        return return_code
-
-    evaluation_tasks = [x.strip() for x in iniinfo["_evaluation"].split(",")]
-    evaluation_scripts = inspect.getmembers(evaluation, inspect.ismodule)
-
-    return_codes = []
-    for task in evaluation_tasks:
-        task_module = None
-        for script_name, script_module in evaluation_scripts:
-            if task == script_name and hasattr(script_module,"evaluate"):
-                if script_module.evaluate._isEvaluator: # check if script is decorated with @evaluation_script
-                    task_module = script_module
-        if task_module is None:
-            raise ImportError("Evaluation script for evaluation task {0} was not found"\
-                            .format(task))
-        print("Running {} evaluator".format(task))
-        return_code = task_module.evaluate(iniinfo,runtime)
-        if return_code == 0:
-            print(" - passed\n")
-        else:
-            print(" - failed with code {}\n".format(return_code))
-        return_codes.append(return_code)
-
-    if any(r != 0 for r in return_codes):
-        print("At least one evaluation task failed!")
-        print("--- test failed ---")
-        return 1
-    else:
-        print("--- test passed ---")
-        return 0

python/testtools/setup.py

@@ -5,7 +5,7 @@ from setuptools import setup
 
 
 def dorie_testtools_scripts():
-    return ['./wrapper/test_dorie.py','./wrapper/test_dorie_pfg.py']
+    return ['./wrapper/test_dorie.py']
 
 setup(name='dorie.testtools',
       version='0.1',
@@ -14,6 +14,6 @@ setup(name='dorie.testtools',
       author='Dion Häfner <mail@dionhaefner.de>',
       author_email='dorieteam@iup.uni-heidelberg.de',
       url='',
-      packages=['dorie.testtools','dorie.testtools.dorie', 'dorie.testtools.dorie_pfg', 'dorie.testtools.utilities','dorie.testtools.wrapper'],
+      packages=['dorie.testtools'],
       install_requires=['dune.testtools'],
       scripts=dorie_testtools_scripts())

python/testtools/wrapper/CMakeLists.txt

 configure_file(test_dorie.py.in ${CMAKE_CURRENT_SOURCE_DIR}/test_dorie.py)
-configure_file(test_dorie_pfg.py.in ${CMAKE_CURRENT_SOURCE_DIR}/test_dorie_pfg.py)

python/testtools/wrapper/test_dorie_pfg.py.in

-#!/usr/bin/env python
-from __future__ import absolute_import
-
-import sys
-import os
-
-from dune.testtools.wrapper.argumentparser import get_args
-from dune.testtools.parser import parse_ini_file
-from dorie.testtools.wrapper import test_dorie_pfg
-
-# paths set by cmake
-DORIEDIR = "@CMAKE_BINARY_DIR@"
-#
-
-DORIE_WRAPPER = os.path.join(DORIEDIR, "bin/dorie")
-
-if __name__ == "__main__":
-    args = get_args()
-    iniargument = args["ini"]
-    iniinfo = parse_ini_file(args["ini"])
-    sys.exit(test_dorie_pfg.test_dorie_pfg(iniinfo,iniargument,DORIE_WRAPPER))

python/utilities/dorie/utilities/fuzzy_compare_grid.py

@@ -10,7 +10,6 @@ def compare(grid1,grid2,abstol=1E-6,reltol=1E-3,strict=False):
 
     def sort_grid(grid):
         new_shape = (grid.cellCenters().shape[0],-1)
-        print(grid.cellCenters().shape)
         cells = grid.cellCenters().reshape(*new_shape)
         ix = np.lexsort(cells)
         sorted_cells = np.array([c[ix] for c in cells])

testing/CMakeLists.txt

 message(STATUS "Handling system tests")
 
-#configure_file(convergence.mini.in ${CMAKE_CURRENT_LIST_DIR}/convergence.mini)
-#dune_add_system_test(TARGET dorie INIFILE convergence.mini SCRIPT test_dorie.py)
-
-configure_file(ode.mini.in ${CMAKE_CURRENT_LIST_DIR}/ode.mini)
-dune_add_system_test(TARGET dorie INIFILE ode.mini SCRIPT test_dorie.py)
-
-configure_file(ode_higherorder.mini.in ${CMAKE_CURRENT_LIST_DIR}/ode_higherorder.mini)
-dune_add_system_test(TARGET dorie INIFILE ode_higherorder.mini SCRIPT test_dorie.py)
-
-configure_file(parfield_muphi.mini.in ${CMAKE_CURRENT_LIST_DIR}/parfield_muphi.mini)
-dune_add_system_test(TARGET dorie-pfg INIFILE parfield_muphi.mini SCRIPT test_dorie_pfg.py)
-
-configure_file(muphi.mini.in ${CMAKE_CURRENT_LIST_DIR}/muphi.mini)
-dune_add_system_test(TARGET dorie INIFILE muphi.mini SCRIPT test_dorie.py)
-set_property(TEST dorie_muphi APPEND PROPERTY DEPENDS dorie-pfg_muphi_pfg)
-
-configure_file(reference_2d.mini.in ${CMAKE_CURRENT_LIST_DIR}/reference_2d.mini)
-dune_add_system_test(TARGET dorie INIFILE reference_2d.mini SCRIPT test_dorie.py)
-
-configure_file(reference_3d.mini.in ${CMAKE_CURRENT_LIST_DIR}/reference_3d.mini)
-dune_add_system_test(TARGET dorie INIFILE reference_3d.mini SCRIPT test_dorie.py)
-
-configure_file(parfield.mini.in ${CMAKE_CURRENT_LIST_DIR}/parfield.mini)
-dune_add_system_test(TARGET dorie-pfg INIFILE parfield.mini SCRIPT test_dorie_pfg.py)
-
-configure_file(correlation.mini.in ${CMAKE_CURRENT_LIST_DIR}/correlation.mini)
-dune_add_system_test(TARGET dorie-pfg INIFILE correlation.mini SCRIPT test_dorie_pfg.py)
+function(dorie_add_system_test target metaini)
+	configure_file(${metaini}.in ${CMAKE_CURRENT_LIST_DIR}/${metaini})
+	dune_add_system_test(TARGET ${target} INIFILE ${metaini} SCRIPT test_dorie.py)
+endfunction()
+
+function(dorie_add_system_test_dependency test1 test2)
+	set_tests_properties(${test1} PROPERTIES DEPENDS ${test2})
+endfunction()
+
+# dorie run
+dorie_add_system_test(dorie ode.mini)
+dorie_add_system_test(dorie ode_higherorder.mini)
+dorie_add_system_test(dorie muphi.mini)
+dorie_add_system_test_dependency(dorie_muphi dorie-pfg_muphi_pfg)
+dorie_add_system_test(dorie reference_2d.mini)
+dorie_add_system_test(dorie reference_3d.mini)
+
+# dorie pfg
+dorie_add_system_test(dorie-pfg parfield.mini)
+dorie_add_system_test(dorie-pfg parfield_muphi.mini)
+#dorie_add_system_test(dorie-pfg correlation.mini)
+
+# dorie plot
+dorie_add_system_test(dorie plot.mini)
+dorie_add_system_test_dependency(dorie_plot dorie_reference_2d_0000)
+
+# dorie create
+dorie_add_system_test(dorie create.mini)

testing/convergence.mini.in

-include ${CMAKE_BINARY_DIR}/doc/default_files/config.ini
-
-__name = convergence
-__inifile_optionkey = run
-
-_asset_path = "${CMAKE_CURRENT_LIST_DIR}"
-_evaluation = convergence
-_convergence.minTime = 5E5
-
-output.fileName = convergence | unique
-output.outputPath = convergence | unique
-output.verbose = 0
-
-time.end = 1E6
-time.maxTimestep = 1E5
-time.startTimestep = 1E4
-
-adaptivity.threshold = 1E-10
-adaptivity.useAdaptivity = true
-adaptivity.refinementFraction = .05
-
-grid.initialLevel = 0
-grid.gridType = gmsh, rectangular | expand
-grid.cells = 20 20
-grid.gridFile = "{_asset_path}/meshes/mesh.msh"
-
-boundary.file = "{_asset_path}/bcs/bcFile2d.dat"
-
-parameters.arrayFile = "{_asset_path}/parfields/fftfield.h5", "{_asset_path}/parfields/fftfield-miller.h5" | expand