Mod: improved logger output

Fix: mistakes in samples
Mod: Few images for docs
Mod: improved cli

.gitignore

@@ -16,6 +16,5 @@ env/
 *.run.xml
 *.synctex.gz
 *.toc
-*.png
 *.out
 *.egg-info

anisotropy/__init__.py

@@ -26,6 +26,7 @@ env.update(
 )
 env.update(
     logger_name = "anisotropy",
+    db_name = "anisotropy",
     db_path = env["BUILD"],
     salome_timeout = 15 * 60,
     openfoam_template = os.path.join(env["ROOT"], "anisotropy/openfoam/template")

anisotropy/core/cli.py

@@ -81,6 +81,16 @@ def anisotropy():
     default = 1,
     help = "Count of parallel processes"
 )
+@click.option(
+    "-D", "--database", "database",
+    help = "Database path"
+)
+@click.option(
+    "-f", "--force", "force",
+    type = click.BOOL,
+    default = False,
+    help = "Overwrite existing entries"
+)
 @click.option(
     "-p", "--param", "params", 
     metavar = "key=value", 
@@ -88,8 +98,8 @@ def anisotropy():
     cls = KeyValueOption,
     help = "Overwrite existing parameter (except control variables)"
 )
-def compute(stage, nprocs, params):
-    from anisotropy.core.main import Anisotropy, logger
+def compute(stage, nprocs, database, force, params):
+    from anisotropy.core.main import Anisotropy, Database, logger
     from anisotropy.core.utils import timer, parallel
 
     args = dict()
@@ -99,14 +109,31 @@ def compute(stage, nprocs, params):
 
     ###
     model = Anisotropy()
+
+    if database:
+        if database[-3: ] == ".db":
+            splitted = database.split("/")
+            db_path = "/".join(splitted[ :-1])
+            db_name = splitted[-1: ][0][ :-3]
+
+        else:
+            raise Exception("Invalid database extension")
+
+        model.db = Database(db_name, db_path)
+        
+    logger.info("Constructing database, tables ...")
     model.db.setup()
 
+    def fill_db():
         if model.db.isempty():
             paramsAll = model.loadFromScratch()
 
             for entry in paramsAll:
                 model.db.update(entry)
 
+    _, fill_elapsed = timer(fill_db)()
+    logger.info(f"Elapsed time = { fill_elapsed }")
+
     ###
     def computeCase(stage, type, direction, theta):
         case = Anisotropy()
@@ -114,11 +141,15 @@ def compute(stage, nprocs, params):
         case.evalParams()
         case.update()
 
+        logger.info(f"Case: type = { type }, direction = { direction }, theta = { theta }")
+        logger.info(f"Stage: { stage }")
+
         if stage == "all" or stage == "mesh":
+            if not case.params.get("meshresult", {}).get("status") == "Done" or force:
                 (out, err, returncode), elapsed = timer(case.computeMesh)()
 
-            click.echo(out)
-            click.echo(err)
+                if out: logger.info(out)
+                if err: logger.error(err)
 
                 case.load(type, direction, theta)
 
@@ -130,11 +161,15 @@ def compute(stage, nprocs, params):
                     logger.error("Mesh computation failed. Skipping flow computation ...")
                     return
 
+            else:
+                logger.info("Mesh exists. Skipping ...")
+
         if stage == "all" or stage == "flow":
+            if not case.params.get("flowresult", {}).get("status") == "Done" or force:
                 (out, err, returncode), elapsed = timer(case.computeFlow)()
 
-            click.echo(out)
-            click.echo(err)
+                if out: logger.info(out)
+                if err: logger.error(err)
 
                 case.load(type, direction, theta)
 
@@ -146,6 +181,9 @@ def compute(stage, nprocs, params):
                     logger.error("Flow computation failed.")
                     return
 
+            else:
+                logger.info("Flow exists. Skipping ...")
+
 
     ###
     params = model.db.loadGeneral(

anisotropy/core/main.py

@@ -27,8 +27,8 @@ from anisotropy.samples import Simple, FaceCentered, BodyCentered
 logger = logging.getLogger(env["logger_name"])
 setupLogger(logger, logging.INFO, env["LOG"])
 
-peeweeLogger = logging.getLogger("peewee")
-peeweeLogger.setLevel(logging.INFO)
+#peeweeLogger = logging.getLogger("peewee")
+#peeweeLogger.setLevel(logging.INFO)
 
 
 class Anisotropy(object):
@@ -38,7 +38,7 @@ class Anisotropy(object):
         """Constructor method"""
 
         self.env = env
-        self.db = Database("anisotropy", env["db_path"])
+        self.db = Database(self.env["db_name"], self.env["db_path"])
         self.params = []
 
 
@@ -245,7 +245,7 @@ class Anisotropy(object):
             *salomeargs, 
             timeout = self.env["salome_timeout"],
             root = self.env["ROOT"],
-            logpath = os.path.join(self.env["LOG"], "salome.log")
+            logpath = self.env["LOG"]
         )
 
 
@@ -260,20 +260,14 @@ class Anisotropy(object):
 
         p = self.params
 
-        logger.info("\n".join([
-            "genmesh:",
-            f"structure type:\t{ p['structure']['type'] }",
-            f"coefficient:\t{ p['structure']['theta'] }",
-            f"fillet:\t{ p['structure']['fillets'] }",
-            f"flow direction:\t{ p['structure']['direction'] }"
-        ]))
-
         salome.salome_init()
 
 
         ###
         #   Shape
         ##
+        logger.info("Constructing shape ...")
+
         geompy = salomepl.geometry.getGeom()
         structure = dict(
             simple = Simple,
@@ -284,17 +278,12 @@ class Anisotropy(object):
 
         [length, surfaceArea, volume] = geompy.BasicProperties(shape, theTolerance = 1e-06)
 
-        logger.info("\n".join([
-            "shape:",
-            f"edges length:\t{ length }",
-            f"surface area:\t{ surfaceArea }",
-            f"volume:\t{ volume }"
-        ]))
-
 
         ###
         #   Mesh
         ##
+        logger.info("Prepairing mesh ...")
+
         mp = p["mesh"]
 
         lengths = [
@@ -332,6 +321,7 @@ class Anisotropy(object):
 
 
         self.update()
+        logger.info("Computing mesh ...")
         out, err, returncode = mesh.compute()
 
         ###
@@ -345,6 +335,7 @@ class Anisotropy(object):
 
             casePath = self.getCasePath()
             os.makedirs(casePath, exist_ok = True)
+            logger.info("Exporting mesh ...")
             mesh.exportUNV(os.path.join(casePath, "mesh.unv"))
 
             meshStats = mesh.stats()
@@ -356,10 +347,6 @@ class Anisotropy(object):
             )
             self.update()
 
-            logger.info("mesh stats:\n{}".format(
-                "\n".join(map(lambda v: f"{ v[0] }:\t{ v[1] }", meshStats.items()))
-            ))
-
         else:
             logger.error(err)
 
@@ -389,6 +376,11 @@ class Anisotropy(object):
 
         # ISSUE: ideasUnvToFoam cannot import mesh with '-case' flag so 'os.chdir' for that
         casePath = self.getCasePath()
+
+        if not os.path.exists(casePath):
+            logger.warning(f"Cannot find case path. Skipping computation ...\n\t{ casePath }")
+            return "", "", 1
+
         os.chdir(casePath)
         openfoam.foamClean()
 
@@ -404,7 +396,7 @@ class Anisotropy(object):
         if not os.path.exists("mesh.unv"):
             logger.error(f"missed 'mesh.unv'")
             os.chdir(self.env["ROOT"])
-            return 1
+            return "", "", 1
 
         out, err, returncode = openfoam.ideasUnvToFoam("mesh.unv")
 
@@ -499,8 +491,6 @@ class Anisotropy(object):
         #    )
         
         out, err, returncode = openfoam.simpleFoam()
-        if out:
-            logger.info(out)
 
         ###
         #   Results
@@ -521,8 +511,7 @@ class Anisotropy(object):
 
         else:
             self.params["flowresult"].update(
-                status = "Failed",
-                flowRate = flowRate
+                status = "Failed"
             )
 
 
@@ -530,6 +519,6 @@ class Anisotropy(object):
 
         os.chdir(self.env["ROOT"])
         
-        return out, err, returncode
+        return out, str(err, "utf-8"), returncode
 
     

anisotropy/core/utils.py

@@ -48,7 +48,7 @@ def setupLogger(logger, level: int, filepath: str = None):
     :param filepath: Path to directory
     :type filepath: str, optional
     """
-
+    logger.handlers = []
     logger.setLevel(level)
 
     streamhandler = logging.StreamHandler()

anisotropy/openfoam/application.py

@@ -42,9 +42,9 @@ def application(name: str, *args: str, case: str = None, stderr: bool = True, us
         out, err = p.communicate()
         logfile.write(err)
 
-        if err and stderr:
-            logger.error("""{}:
-            {}""".format(name, str(err, "utf-8")))
+        #if err and stderr:
+        #    logger.error("""{}:
+        #    {}""".format(name, str(err, "utf-8")))
 
     return out, err, p.returncode
 

anisotropy/openfoam/solvers.py

@@ -8,10 +8,12 @@ import re
 
 def potentialFoam(case: str = None, useMPI: bool = False):
     if useMPI:
-        application("potentialFoam", "-parallel", useMPI = True, case = case, stderr = True)
+        out, err, returncode = application("potentialFoam", "-parallel", useMPI = True, case = case, stderr = True)
 
     else:
-        application("potentialFoam", case = case, stderr = True)
+        out, err, returncode = application("potentialFoam", case = case, stderr = True)
+
+    return out, err, returncode
 
 
 def simpleFoam(case: str = None, useMPI: bool = False):

anisotropy/samples/faceCentered.py

@@ -155,13 +155,13 @@ class FaceCentered(object):
         xy = geompy.MakeVectorDXDYDZ(1, 1, 0)
         xmy = geompy.MakeVectorDXDYDZ(1, -1, 0)
 
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos1), radius)
+        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos1), self.radius)
         lattice1 = geompy.MakeMultiTranslation2D(grain, xy, length, xn, xmy, length, yn)
-        lattice1 = geompy.MakeMultiTranslation1D(lattice1, oz, L, zn - 1)
+        lattice1 = geompy.MakeMultiTranslation1D(lattice1, oz, self.L, zn - 1)
 
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos2), radius)
+        grain = geompy.MakeSpherePntR(geompy.MakeVertex(*spos2), self.radius)
         lattice2 = geompy.MakeMultiTranslation2D(grain, xy, length, xn + 1, xmy, length, yn + 1)
-        lattice2 = geompy.MakeMultiTranslation1D(lattice2, oz, L, zn)
+        lattice2 = geompy.MakeMultiTranslation1D(lattice2, oz, self.L, zn)
         
         grains = geompy.ExtractShapes(lattice1, geompy.ShapeType["SOLID"], True)
         grains += geompy.ExtractShapes(lattice2, geompy.ShapeType["SOLID"], True)