mod: minor changes

anisotropy/cli/cli.py

@@ -135,7 +135,6 @@ def compute(path, configFile, nprocs, stage, overwrite, params, verbose, executi
         if v is not None:
             config.update(**{ k: v })
 
-    print(config.options)
     if pid:
         pid = pathlib.Path(pid).resolve()
 

anisotropy/core/postprocess.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 import pathlib
+import numpy as np
 
 import anisotropy.openfoam as of
 
@@ -15,3 +16,82 @@ def flowRate(patch: str, path: str = None):
     surfaceFieldValue = of.conversion.read_dat(outfile)["sum(phi)"][-1]
 
     return surfaceFieldValue
+
+
+def permeability(viscosity = None, flowRate = None, length = None, areaCross = None, pressureInlet = None, pressureOutlet = None, **kwargs):
+    viscosity = kwargs.get("viscosity", viscosity)
+    flowRate = kwargs.get("flowRate", flowRate)
+    length = kwargs.get("length", length)
+    areaCross = kwargs.get("areaCross", areaCross)
+    pressureInlet = kwargs.get("pressureInlet", pressureInlet)
+    pressureOutlet = kwargs.get("pressureOutlet", pressureOutlet)
+
+    return viscosity * length * flowRate / (areaCross * (pressureInlet - pressureOutlet))
+
+
+def mean_nan(arr):
+    temp = arr.copy()
+
+    if np.isnan(temp[0]):
+        temp[0] = temp[1]
+
+    for n, item in enumerate(temp):
+        if np.all(np.isnan(item)):
+            
+            vals = temp[n - 1 : n + 2]
+
+            if np.sum(~np.isnan(vals)) <= 1:
+                vals = temp[n - 2 : n + 3]
+
+            temp[n] = vals[~np.isnan(vals)].mean()
+
+    return temp
+
+
+def filter_group(arr, nan = True, qhigh = True, quantile = 0.97):
+    temp = arr.copy()
+    check = True
+    quan = np.quantile(temp[~np.isnan(temp)], quantile)
+    limit = 1000
+
+    while check:
+        if nan and np.any(np.isnan(temp)):
+            temp = mean_nan(temp)
+            check = True
+        
+        elif qhigh and np.any(quan < temp):
+            temp[quan < temp] = np.nan
+            check = True
+
+        else:
+            check = False 
+        
+        if limit <= 0:
+            break
+
+        else:
+            limit -= 1
+
+    return temp
+
+
+def pad_nan(x, y):
+    return np.pad(y, (0, x.size - y.size), 'constant', constant_values = np.nan)
+
+
+"""
+def multiplot_y(
+    x, 
+    y,
+    labels = [],
+    lines = [],
+    axes_labels = ["", ""],
+    legend = True,
+    grid = True,
+    figsize = (12, 6)
+    ):
+    fig, ax = plt.subplots(nrows = 1, ncols = 1, figsize = figsize)
+
+    for n, y_arr in enumerate(y):
+        ax.plot(x, y_arr, )
+"""

anisotropy/core/runner.py

@@ -189,7 +189,16 @@ class UltimateRunner(object):
             shapeParams.shapeStatus = "done"
             shapeParams.volume = shape.shape.volume * np.prod(params["scale"])
             shapeParams.volumeCell = shape.cell.volume * np.prod(params["scale"])
+            shapeParams.radius = shape.radius
+            shapeParams.fillets = shape.fillets
             shapeParams.porosity = shapeParams.volume / shapeParams.volumeCell
+            shapeParams.areaOutlet = np.sum([ 
+                face.mass for face in shape.shape.faces if face.name == "outlet" 
+            ]) * params["scale"][0] ** 2
+            shapeParams.length = shape.length * params["scale"][0]
+            shapeParams.areaCellOutlet = np.sum([ 
+                face.mass for face in shape.cell.faces if face.name == "outlet" 
+            ]) * params["scale"][0] ** 2
 
         #   commit parameters
         shapeParams.shapeExecutionTime = timer.elapsed()
@@ -327,7 +336,7 @@ class UltimateRunner(object):
         for current in stages:
             if current == "shape":
                 params = self._query_database("shape")
-
+                
                 #   check database entry
                 if params.shapeStatus == "done" and self.config["overwrite"] is not True:
                     logger.info("Successful shape entry exists, skipping ...")

anisotropy/database/database.py

@@ -6,6 +6,7 @@ from numpy import ndarray
 import peewee as pw
 import pathlib
 import time
+import pandas as pd
 
 from . import tables 
 
@@ -255,3 +256,54 @@ class Database(pw.SqliteDatabase):
                 table = query.get() if query.exists() else None
 
         return table
+
+    def load(
+        self, 
+        field: str,
+        execution: int = None,
+        label: str = None, 
+        direction: list[float] | ndarray = None
+    ):
+        execution = execution or self.getLatest()
+
+        for table in self.tables:
+            try:
+                column = getattr(table, field)
+            
+            except AttributeError:
+                pass
+
+            else:
+                break
+
+        query = table.select(tables.Shape.alpha, column, tables.Shape.direction, tables.Shape.label)
+
+        for current in reversed(self.tables[ :self.tables.index(table)]):
+            query = query.join(table, pw.JOIN.LEFT_OUTER)
+            
+        query = (
+            query.switch(tables.Shape)
+            .where(tables.Shape.exec_id == execution)
+            .order_by(tables.Shape.label, tables.Shape.direction, tables.Shape.alpha)
+        )
+        resp = None
+
+        with self:
+            if query.exists():
+                resp = []
+                for row in query.dicts():
+                    for k in row.keys():
+                        if type(row[k]) == list:
+                            row[k] = str(row[k])
+
+                    resp.append(row)
+            
+        resp = pd.DataFrame(resp)
+
+        if label is not None:
+            resp = resp[resp.label == label]
+        
+        if direction is not None:
+            resp = resp[resp.direction == direction]
+        
+        return resp[field]

anisotropy/database/tables.py

@@ -42,6 +42,10 @@ class Shape(pw.Model):
     volume = pw.FloatField(null = True)
     porosity = pw.FloatField(null = True)
 
+    areaOutlet = pw.FloatField(null = True)
+    length = pw.FloatField(null = True)
+    areaCellOutlet = pw.FloatField(null = True)
+
     class Meta:
         database = database_proxy
         table_name = "shapes"

anisotropy/shaping/primitives.py

@@ -31,6 +31,7 @@ def simple(alpha: float, direction: list | ndarray, **kwargs) -> Periodic:
     pc.__dict__.update(kwargs)
     pc.L = 2 * pc.r0
     pc.direction = np.asarray(direction)
+    pc.length = 0.
 
     #   additional attributes
     pc.cell: ng_occ.Solid = None
@@ -130,6 +131,7 @@ def simple(alpha: float, direction: list | ndarray, **kwargs) -> Periodic:
 
     vecFlow = utils.normal(inletface)
     pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
     
     #   Boundary faces
     symetryId = 0
@@ -189,6 +191,7 @@ def body_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic
     #   additional attributes
     pc.cell: ng_occ.Solid = None
     pc.lattice: ng_occ.Solid = None
+    pc.length = 0.
 
     #   constants   
     zero = ng_occ.Pnt(0, 0, 0)
@@ -292,6 +295,7 @@ def body_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic
 
     vecFlow = utils.normal(inletface)
     pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
     
     #   Boundary faces
     symetryId = 0
@@ -347,6 +351,7 @@ def face_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic
     pc.__dict__.update(kwargs)
     pc.L = pc.r0 * 4 / np.sqrt(2)
     pc.direction = np.asarray(direction)
+    pc.length = 0.
 
     #   additional attributes
     pc.cell: ng_occ.Solid = None
@@ -374,7 +379,6 @@ def face_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic
                 x = x0 + xn * 2 * pc.r0
                 x2 = x20 + xn * 2 * pc.r0 + pc.r0
 
-                # TODO: fix rotations (arcs intersection -> incorrect boolean operations
                 spheres.append(
                     ng_occ.Sphere(ng_occ.Pnt(x, y, z), pc.radius)
                     .Rotate(ng_occ.Axis(ng_occ.Pnt(x, y, z), ng_occ.X), 45)
@@ -471,6 +475,7 @@ def face_centered(alpha: float, direction: list | ndarray, **kwargs) -> Periodic
 
     vecFlow = utils.normal(inletface)
     pc.cell = inletface.Extrude(extr, ng_occ.Vec(*vecFlow))
+    pc.length = extr
     
     #   Boundary faces
     symetryId = 0

poetry.lock

@@ -145,7 +145,7 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
 
 [[package]]
 name = "coverage"
-version = "6.3.1"
+version = "6.3.2"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -421,6 +421,18 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "lz"
+version = "0.11.1"
+description = "\"Lazy\" calculations support."
+category = "main"
+optional = false
+python-versions = ">=3.5.3"
+
+[package.dependencies]
+paradigm = ">=0.6.2,<1.0"
+reprit = ">=0.3.1,<1.0"
+
 [[package]]
 name = "markupsafe"
 version = "2.0.1"
@@ -456,6 +468,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "memoir"
+version = "0.0.3"
+description = "Memoization support."
+category = "main"
+optional = false
+python-versions = ">=3.5.3"
+
 [[package]]
 name = "meshio"
 version = "5.3.0"
@@ -479,6 +499,31 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "mypy"
+version = "0.931"
+description = "Optional static typing for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+mypy-extensions = ">=0.4.3"
+tomli = ">=1.1.0"
+typing-extensions = ">=3.10"
+
+[package.extras]
+dmypy = ["psutil (>=4.0)"]
+python2 = ["typed-ast (>=1.4.0,<2)"]
+
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "numpy"
 version = "1.22.2"
@@ -519,6 +564,19 @@ pytz = ">=2020.1"
 [package.extras]
 test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
+[[package]]
+name = "paradigm"
+version = "0.6.2"
+description = "Python objects metadata parser."
+category = "main"
+optional = false
+python-versions = ">=3.5.3"
+
+[package.dependencies]
+memoir = ">=0.0.3,<1.0"
+mypy = {version = ">=0.812,<1.0", markers = "platform_python_implementation != \"PyPy\""}
+reprit = ">=0.3.1,<1.0"
+
 [[package]]
 name = "pathtools"
 version = "0.1.2"
@@ -747,6 +805,14 @@ category = "dev"
 optional = true
 python-versions = ">=3.6"
 
+[[package]]
+name = "reprit"
+version = "0.6.0"
+description = "Auto __repr__ method generation."
+category = "main"
+optional = false
+python-versions = ">=3.5.3"
+
 [[package]]
 name = "requests"
 version = "2.27.1"
@@ -969,6 +1035,14 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "typing-extensions"
+version = "4.1.1"
+description = "Backported and Experimental Type Hints for Python 3.6+"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "urllib3"
 version = "1.26.8"
@@ -1075,7 +1149,7 @@ gui = ["dash", "dash-bootstrap-components", "dash-vtk"]
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.9,<3.11"
-content-hash = "9d38bd5da0ffac15f137cbbb7d4fbb7448aaf88ec77370f5361fa0b1a2e8ae68"
+content-hash = "6bde8dbd6b2431799fef60413d84962c500bc934457dd2f514e14932bdd0596b"
 
 [metadata.files]
 aiohttp = [
@@ -1250,47 +1324,47 @@ commonmark = [
     {file = "commonmark-0.9.1.tar.gz", hash = "sha256:452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60"},
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+]
 urllib3 = [
     {file = "urllib3-1.26.8-py2.py3-none-any.whl", hash = "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed"},
     {file = "urllib3-1.26.8.tar.gz", hash = "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"},

pyproject.toml

@@ -41,6 +41,7 @@ dash-bootstrap-components = {version = "^1.0.2", optional = true, extras = ["gui
 meshio = "^5.2.2"
 vtk = "^9.1.0"
 dash-vtk = {version = "^0.0.9", optional = true, extras = ["gui"]}
+lz = "^0.11.1"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.5"