New: mesh visualization

New: data visualization
Mod: python deps
This commit is contained in:
L-Nafaryus 2022-01-11 22:57:19 +05:00
parent 3eb1029cb5
commit 479e7d666a
No known key found for this signature in database
GPG Key ID: C76D8DCD2727DBB7
8 changed files with 960 additions and 15 deletions

View File

@ -159,13 +159,17 @@ def init(path, verbose):
help = "Specify log file path"
)
def compute(path, configFile, nprocs, stage, overwrite, params, verbose, execution, pid, logfile):
import anisotropy
from anisotropy.core.runner import UltimateRunner
from anisotropy.core.config import DefaultConfig
from anisotropy.core.utils import setupLogger
anisotropy.loadEnv()
if path:
os.makedirs(os.path.abspath(path), exist_ok = True)
os.chdir(os.path.abspath(path))
os.environ["ANISOTROPY_CWD"] = path
setupLogger(verboseLevel(verbose), logfile)
logger = logging.getLogger(__name__)

View File

@ -114,7 +114,7 @@ class UltimateRunner(object):
execution = "execution-{}".format(self.exec_id)
case = "{}-[{},{},{}]-{}".format(params["label"], *[ str(d) for d in params["direction"] ], params["alpha"])
dirpath = path.join(self.config["build"], execution, case)
dirpath = path.join(os.environ["ANISOTROPY_CWD"], self.config["build"], execution, case)
return path.abspath(dirpath)
@ -216,6 +216,7 @@ class UltimateRunner(object):
if not returncode:
os.makedirs(self.casepath(), exist_ok = True)
out, err, returncode = self.mesh.export(path.join(self.casepath(), filename))
out, err, returncode = self.mesh.export(path.join(self.casepath(), "mesh.msh"))
if not returncode:
meshParams.meshStatus = "done"

View File

@ -0,0 +1,96 @@
# -*- coding: utf-8 -*-
# This file is part of anisotropy.
# License: GNU GPL version 3, see the file "LICENSE" for details.
from dash.dash_table import DataTable
from dash import html
from dash import dcc
import dash_bootstrap_components as dbc
from dash.dependencies import Input, Output, State
import os
from .app import app
from .styles import *
###
# Layout
##
layout = html.Div([
# Messages and timer
dbc.Alert(
id = "db_status",
duration = 10000,
dismissable = True,
is_open = False,
style = message
),
#dcc.Interval(id = "interval", interval = 1000, n_intervals = 0),
# Query
html.H2("Database"),
html.Hr(),
html.P("Query"),
dcc.Textarea(id = "db_input", style = { "min-width": "100%"}),
html.Br(),
dbc.Button("Query", id = "query", style = minWidth),
# Output
html.Hr(),
html.P("Output"),
DataTable(id = "db_output", columns = [], data = [], style_table = { "overflow": "scroll"}, style_cell={
'textAlign': 'left',
'width': '150px',
'minWidth': '180px',
'maxWidth': '180px',
'whiteSpace': 'no-wrap',
'overflow': 'hidden',
'textOverflow': 'ellipsis',
}),
])
###
# Callbacks
##
@app.callback(
Output("db_output", "columns"),
Output("db_output", "data"),
Output("db_status", "children"),
Output("db_status", "is_open"),
Output("db_status", "color"),
[ Input("query", "n_clicks") ],
[ State("db_input", "value") ],
prevent_initial_call = True
)
def db_query(clicks, db_input):
from anisotropy.database import Database
from peewee import OperationalError
dbpath = os.path.join(os.environ["ANISOTROPY_CWD"], os.environ["ANISOTROPY_DB_FILE"])
db = Database(path = dbpath)
try:
db.connect()
cursor = db.execute_sql(db_input)
except OperationalError as e:
db.close()
return None, None, str(e), True, "danger"
else:
columns = [ { "name": col[0], "id": col[0] } for col in cursor.description ]
data = []
for row in cursor.fetchall():
item = {}
for key, value in zip(columns, row):
item[key["name"]] = value
data.append(item)
db.close()
return columns, data, "", False, "success"

View File

@ -10,6 +10,8 @@ import dash_bootstrap_components as dbc
from . import (
runner,
settings,
database,
visualization,
about
)
from .app import app
@ -31,6 +33,8 @@ app.layout = html.Div([
dbc.Nav([
dbc.NavLink("Runner", href = "/", active = "exact", style = white),
dbc.NavLink("Settings", href = "/settings", active = "exact", style = white),
dbc.NavLink("Database", href = "/database", active = "exact", style = white),
dbc.NavLink("Visualization", href = "/visualization", active = "exact", style = white),
dbc.NavLink("About", href = "/about", active = "exact", style = white),
], vertical = True, pills = True),
@ -68,6 +72,12 @@ def displayPage(pathname):
elif pathname == "/about":
return about.layout
elif pathname == "/database":
return database.layout
elif pathname == "/visualization":
return visualization.layout
else:
return runner.layout

View File

@ -0,0 +1,347 @@
# -*- coding: utf-8 -*-
# This file is part of anisotropy.
# License: GNU GPL version 3, see the file "LICENSE" for details.
from dash.dash_table import DataTable
from dash import html
from dash import dcc
import dash_bootstrap_components as dbc
from dash.dependencies import Input, Output, State
import dash_vtk
import dash_vtk.utils
import vtk
import os
from .app import app
from . import styles
class MeshRepresentation(object):
def __init__(self, path):
self.mesh = vtk.vtkXMLUnstructuredGridReader()
self.mesh.SetFileName(path)
self.mesh.Update()
self.clip = False
self.crinkle = False
self.wireframe = True
self.planeNormal = [0, 0, -1]
self.planeOrigin = [0, 0, 1]
def getRepresentation(self):
if not self.clip:
dataset = self.mesh.GetOutput()
else:
plane = vtk.vtkPlane()
plane.SetNormal(self.planeNormal)
plane.SetOrigin(self.planeOrigin)
if self.crinkle:
implfunc = vtk.vtkImplicitBoolean()
implfunc.AddFunction(plane)
implfunc.Modified()
clipper = vtk.vtkExtractGeometry()
clipper.SetInputConnection(self.mesh.GetOutputPort())
clipper.SetImplicitFunction(implfunc)
clipper.SetExtractInside(1)
clipper.SetExtractOnlyBoundaryCells(0)
clipper.SetExtractBoundaryCells(1)
clipper.ExtractInsideOff()
else:
clipper = vtk.vtkTableBasedClipDataSet()
clipper.SetInputData(self.mesh.GetOutput())
clipper.SetClipFunction(plane)
clipper.SetValue(0.0)
clipper.GenerateClippedOutputOn()
clipper.Update()
dataset = clipper.GetOutput()
representation = dash_vtk.GeometryRepresentation(
id = "mesh-representation",
children = [
dash_vtk.Mesh(id = "mesh", state = dash_vtk.utils.to_mesh_state(dataset))
],
property = { "edgeVisibility": self.wireframe }
)
return representation
###
# Layout
##
controls = html.Div([
html.P("Execution"),
dcc.Input(id = "exec_id", type = "number", value = 0, min = 0, style = styles.minWidth),
html.Br(),
html.P("Structure"),
dcc.Dropdown(
id = "structure",
options = [ { "label": v, "value": v } for v in [ "simple", "bodyCentered", "faceCentered" ] ],
value = "simple",
style = styles.minWidth
),
html.Br(),
html.P("Direction"),
dcc.Dropdown(
id = "direction",
options = [ { "label": str(v), "value": str(v)} for v in [ [1., 0., 0.], [0., 0., 1.], [1., 1., 1.] ] ],
value = str([1., 0., 0.]),
),
html.Br(),
html.P("Alpha"),
dcc.Input(id = "alpha", type = "number", value = 0.01, min = 0.01, step = 0.01, style = styles.minWidth),
html.Br(),
html.P("Clip"),
dbc.Checkbox(id = "clip", value = False),
html.Br(),
html.P("Crinkle"),
dbc.Checkbox(id = "crinkle", value = False),
html.Br(),
html.P("Plane normal"),
dcc.Input(id = "normal-x", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }),
dcc.Input(id = "normal-y", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }),
dcc.Input(id = "normal-z", type = "number", value = -1, style = { "width": "100px", "margin-bottom": "20px" }),
html.Br(),
html.P("Plane origin"),
dcc.Input(id = "origin-x", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }),
dcc.Input(id = "origin-y", type = "number", value = 0, style = { "width": "100px", "margin-bottom": "20px" }),
dcc.Input(id = "origin-z", type = "number", value = 1, style = { "width": "100px", "margin-bottom": "20px" }),
html.Br(),
html.P("Wireframe"),
dbc.Checkbox(id = "wireframe", value = True),
html.Br(),
dbc.Button("Draw", id = "draw"),
])
plotcontrols = html.Div([
html.P("Execution"),
dcc.Input(id = "plot-exec_id", type = "number", value = 0, min = 0, style = styles.minWidth),
html.Br(),
html.P("Structure"),
dcc.Dropdown(
id = "plot-structure",
options = [ { "label": v, "value": v } for v in [ "simple", "bodyCentered", "faceCentered" ] ],
value = "simple"
),
html.Br(),
html.P("Direction"),
dcc.Dropdown(
id = "plot-direction",
options = [ { "label": str(v), "value": str(v)} for v in [ [1., 0., 0.], [0., 0., 1.], [1., 1., 1.], "all" ] ],
value = str([1., 0., 0.]),
),
html.Br(),
html.P("Data"),
dcc.Dropdown(
id = "plot-data",
options = [ { "label": v, "value": v } for v in [ "porosity",] ],
value = "porosity",
),
html.Br(),
dbc.Button("Draw", id = "plot-draw"),
])
layout = html.Div([
html.H2("Plot"),
html.Hr(),
dbc.Container(
fluid = True,
children = [
dbc.Row([
dbc.Col(width = 4, children = plotcontrols, style = { "min-width": "350px" }),
dbc.Col(
width = 8,
children = [
html.Div(id = "plot-output", style = { "width": "100%", "min-width": "800px" })
]
, style = { "min-width": "800px" }),
], style = { "height": "100%"}),
]),
html.Br(),
html.H2("Mesh"),
html.Hr(),
dbc.Container(
fluid = True,
children = [
dbc.Row([
dbc.Col(width = 4, children = controls, style = { "min-width": "350px" }),
dbc.Col(
width = 8,
children = [
html.Div(id = "vtk-output", style = { "height": "800px", "width": "100%", "min-width": "800px" })
]
, style = { "min-width": "800px" }),
], style = { "height": "100%"}),
])
])
@app.callback(
[ Output("plot-output", "children") ],
[ Input("plot-draw", "n_clicks") ],
[
State("plot-exec_id", "value"),
State("plot-structure", "value"),
State("plot-direction", "value"),
State("plot-data", "value"),
]
)
def plotDraw(clicks, execution, structure, direction, data):
from os import path
from peewee import JOIN
from anisotropy.database import Database, models
import json
from pandas import DataFrame
import plotly.express as px
dbpath = path.join(os.environ["ANISOTROPY_CWD"], os.environ["ANISOTROPY_DB_FILE"])
if not path.isfile(dbpath):
return [ "Database not found" ]
db = Database(path = dbpath)
if not db.getExecution(execution):
return [ "Execution not found" ]
for model in db.tables:
try:
column = getattr(model, data)
except AttributeError as e:
pass
else:
break
query = (
models.Shape
.select(models.Shape.alpha, column)
.join(models.Execution, JOIN.LEFT_OUTER)
.switch(models.Shape)
.join(models.Mesh, JOIN.LEFT_OUTER)
.switch(models.Shape)
.where(
models.Shape.exec_id == execution,
models.Shape.label == structure,
models.Shape.direction == json.loads(direction),
)
)
print(query.sql())
with db:
if query.exists():
table = []
for row in query.dicts():
table.append(row)
else:
table = None
if not table:
return [ "Results not found" ]
import plotly.io as plt_io
plt_io.templates["custom_dark"] = plt_io.templates["plotly_dark"]
plt_io.templates["custom_dark"]['layout']['paper_bgcolor'] = '#30404D'
plt_io.templates["custom_dark"]['layout']['plot_bgcolor'] = '#30404D'
plt_io.templates['custom_dark']['layout']['yaxis']['gridcolor'] = '#4f687d'
plt_io.templates['custom_dark']['layout']['xaxis']['gridcolor'] = '#4f687d'
fig = px.line(
DataFrame(table), x = "alpha", y = data, title = structure, markers = True
)
fig.layout.template = "custom_dark"
fig.update_xaxes(showline=True, linewidth=1, linecolor='#4f687d', mirror=True)
fig.update_yaxes(showline=True, linewidth=1, linecolor='#4f687d', mirror=True)
plot = dcc.Graph(
figure = fig
)
return [ plot ]
@app.callback(
[ Output("alpha", "min"), Output("alpha", "max") ],
[ Input("structure", "value") ]
)
def alphaLimits(label):
if label == "simple":
return 0.01, 0.29
elif label == "bodyCentered":
return 0.01, 0.18
elif label == "faceCentered":
return 0.01, 0.13
@app.callback(
[ Output("vtk-output", "children") ],
[ Input("draw", "n_clicks") ],
[
State("exec_id", "value"),
State("structure", "value"),
State("direction", "value"),
State("alpha", "value"),
State("clip", "value"),
State("crinkle", "value"),
State("wireframe", "value"),
State("normal-x", "value"),
State("normal-y", "value"),
State("normal-z", "value"),
State("origin-x", "value"),
State("origin-y", "value"),
State("origin-z", "value"),
],
prevent_initial_call = True
)
def meshDraw(clicks, execution, structure, direction, alpha, clip, crinkle, wireframe, normal_x, normal_y, normal_z, origin_x, origin_y, origin_z):
from os import path
import meshio
execution = "execution-{}".format(execution)
case = "{}-{}-{}".format(structure, direction.replace(" ", ""), alpha)
casepath = path.join(os.environ["ANISOTROPY_CWD"], os.environ["ANISOTROPY_BUILD_DIR"], execution, case)
basemeshpath = path.join(casepath, "mesh.msh")
meshpath = path.join(casepath, "mesh.vtu")
if not path.exists(basemeshpath):
return [ "Mesh not found" ]
if not path.exists(meshpath) or not path.isfile(meshpath):
meshold = meshio.read(basemeshpath)
meshold.write(meshpath)
meshrepr = MeshRepresentation(meshpath)
meshrepr.clip = clip
meshrepr.crinkle = crinkle
meshrepr.wireframe = wireframe
meshrepr.planeNormal = [ normal_x, normal_y, normal_z ]
meshrepr.planeOrigin = [ origin_x, origin_y, origin_z ]
view = dash_vtk.View([ meshrepr.getRepresentation() ])
return [ view ]

View File

@ -66,6 +66,9 @@ class Mesh(object):
elif ext == "mesh":
self.mesh.Export(filename, "Neutral Format")
elif ext == "msh":
self.mesh.Export(filename, "Gmsh2 Format")
else:
raise NotImplementedError(f"Mesh format '{ ext }' is not supported")

507
poetry.lock generated
View File

@ -1,3 +1,34 @@
[[package]]
name = "aiohttp"
version = "3.8.1"
description = "Async http client/server framework (asyncio)"
category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
aiosignal = ">=1.1.2"
async-timeout = ">=4.0.0a3,<5.0"
attrs = ">=17.3.0"
charset-normalizer = ">=2.0,<3.0"
frozenlist = ">=1.1.1"
multidict = ">=4.5,<7.0"
yarl = ">=1.0,<2.0"
[package.extras]
speedups = ["aiodns", "brotli", "cchardet"]
[[package]]
name = "aiosignal"
version = "1.2.0"
description = "aiosignal: a list of registered asynchronous callbacks"
category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
frozenlist = ">=1.1.0"
[[package]]
name = "alabaster"
version = "0.7.12"
@ -14,6 +45,14 @@ category = "dev"
optional = true
python-versions = "*"
[[package]]
name = "async-timeout"
version = "4.0.2"
description = "Timeout context manager for asyncio programs"
category = "main"
optional = false
python-versions = ">=3.6"
[[package]]
name = "atomicwrites"
version = "1.4.0"
@ -26,7 +65,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
name = "attrs"
version = "21.4.0"
description = "Classes Without Boilerplate"
category = "dev"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
@ -67,8 +106,8 @@ python-versions = "*"
name = "charset-normalizer"
version = "2.0.10"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "dev"
optional = true
category = "main"
optional = false
python-versions = ">=3.5.0"
[package.extras]
@ -93,6 +132,17 @@ category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "commonmark"
version = "0.9.1"
description = "Python parser for the CommonMark Markdown spec"
category = "main"
optional = false
python-versions = "*"
[package.extras]
test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
[[package]]
name = "coverage"
version = "6.2"
@ -173,6 +223,18 @@ category = "main"
optional = true
python-versions = "*"
[[package]]
name = "dash-vtk"
version = "0.0.9"
description = "React based declarative usage of vtk.js for Dash"
category = "main"
optional = true
python-versions = "*"
[package.dependencies]
dash = "*"
vtk = "*"
[[package]]
name = "dill"
version = "0.3.4"
@ -265,6 +327,14 @@ ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=13.0.0)"]
woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
[[package]]
name = "frozenlist"
version = "1.2.0"
description = "A list-like structure which implements collections.abc.MutableSequence"
category = "main"
optional = false
python-versions = ">=3.6"
[[package]]
name = "graphviz"
version = "0.13.2"
@ -282,8 +352,8 @@ test = ["mock (>=2)", "pytest (>=3.4,!=3.10.0)", "pytest-mock (>=1.8)", "pytest-
name = "idna"
version = "3.3"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "dev"
optional = true
category = "main"
optional = false
python-versions = ">=3.5"
[[package]]
@ -367,6 +437,29 @@ category = "dev"
optional = false
python-versions = "*"
[[package]]
name = "meshio"
version = "5.2.2"
description = "I/O for many mesh formats"
category = "main"
optional = false
python-versions = ">=3.7"
[package.dependencies]
numpy = "*"
rich = "*"
[package.extras]
all = ["netcdf4", "h5py"]
[[package]]
name = "multidict"
version = "5.2.0"
description = "multidict implementation"
category = "main"
optional = false
python-versions = ">=3.6"
[[package]]
name = "numpy"
version = "1.22.0"
@ -534,8 +627,8 @@ numpy = "*"
name = "pygments"
version = "2.11.2"
description = "Pygments is a syntax highlighting package written in Python."
category = "dev"
optional = true
category = "main"
optional = false
python-versions = ">=3.5"
[[package]]
@ -653,6 +746,22 @@ urllib3 = ">=1.21.1,<1.27"
socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
[[package]]
name = "rich"
version = "11.0.0"
description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
category = "main"
optional = false
python-versions = ">=3.6.2,<4.0.0"
[package.dependencies]
colorama = ">=0.4.0,<0.5.0"
commonmark = ">=0.9.0,<0.10.0"
pygments = ">=2.6.0,<3.0.0"
[package.extras]
jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
[[package]]
name = "setuptools-scm"
version = "6.3.2"
@ -852,6 +961,21 @@ brotli = ["brotlipy (>=0.6.0)"]
secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
[[package]]
name = "vtk"
version = "9.1.0"
description = "VTK is an open-source toolkit for 3D computer graphics, image processing, and visualization"
category = "main"
optional = false
python-versions = "*"
[package.dependencies]
matplotlib = ">=2.0.0"
wslink = ">=1.0.4"
[package.extras]
numpy = ["numpy (>=1.9)"]
[[package]]
name = "vulture"
version = "2.3"
@ -887,6 +1011,29 @@ python-versions = ">=3.6"
[package.extras]
watchdog = ["watchdog"]
[[package]]
name = "wslink"
version = "1.3.1"
description = "Python/JavaScript library for communicating over WebSocket"
category = "main"
optional = false
python-versions = "*"
[package.dependencies]
aiohttp = "*"
[[package]]
name = "yarl"
version = "1.7.2"
description = "Yet another URL library"
category = "main"
optional = false
python-versions = ">=3.6"
[package.dependencies]
idna = ">=2.0"
multidict = ">=4.0"
[extras]
analyze = []
doc = []
@ -895,9 +1042,87 @@ gui = ["dash", "dash-bootstrap-components"]
[metadata]
lock-version = "1.1"
python-versions = ">=3.9,<3.11"
content-hash = "256be009440b09b5c2da236de29cc85c97a48b352921d60dc766df68b359bd16"
content-hash = "d690dac4b444af4dcd5d1c5001ecb445a47d545c93bc91b5a6fd7f88a4a8d994"
[metadata.files]
aiohttp = [
{file = "aiohttp-3.8.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1ed0b6477896559f17b9eaeb6d38e07f7f9ffe40b9f0f9627ae8b9926ae260a8"},
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View File

@ -38,6 +38,9 @@ dill = "^0.3.4"
psutil = "^5.9.0"
dash = {version = "^2.0.0", optional = true, extras = ["gui"]}
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"]}
[tool.poetry.dev-dependencies]
pytest = "^6.2.5"
@ -53,7 +56,7 @@ pytest-json-report = "^1.4.1"
[tool.poetry.extras]
analyze = ["jupyterlab", "seaborn", "sklearn"]
doc = ["Sphinx", "sphinx-rtd-theme", "pydeps", "peewee-erd"]
gui = ["dash", "dash-bootstrap-components"]
gui = ["dash", "dash-bootstrap-components", "dash-vtk"]
[build-system]
requires = ["poetry-core>=1.0.0"]