Merge pull request #32 from dragos-ana/enable_vtu_support

feat: enable vtu file support, improve testing suite, improve design condition rendering

Author: dragos-ana

requirements.txt

@@ -2,25 +2,25 @@
 # This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
-#    pip-compile --all-extras --cert=None --client-cert=None --index-url=None --output-file=requirements.txt --pip-args=None requirements.in
+#    pip-compile --all-extras --output-file=requirements.txt requirements.in
 #
 aiohappyeyeballs==2.6.1
     # via aiohttp
-aiohttp==3.12.15
+aiohttp==3.13.2
     # via wslink
 aiosignal==1.4.0
     # via aiohttp
-attrs==25.3.0
+attrs==25.4.0
     # via aiohttp
-certifi==2025.8.3
+certifi==2025.11.12
     # via
     #   netcdf4
     #   requests
-cfgv==3.4.0
+cfgv==3.5.0
     # via pre-commit
-cftime==1.6.4.post1
+cftime==1.6.5
     # via netcdf4
-charset-normalizer==3.4.3
+charset-normalizer==3.4.4
     # via requests
 contourpy==1.3.3
     # via matplotlib
@@ -30,25 +30,25 @@ deprecation==2.1.0
     # via rapidyaml
 distlib==0.4.0
     # via virtualenv
-filelock==3.19.1
+filelock==3.20.0
     # via virtualenv
-fonttools==4.60.0
+fonttools==4.60.1
     # via matplotlib
-fourcipp==1.18.0
+fourcipp==1.39.0
     # via -r requirements.in
-frozenlist==1.7.0
+frozenlist==1.8.0
     # via
     #   aiohttp
     #   aiosignal
-identify==2.6.14
+identify==2.6.15
     # via pre-commit
-idna==3.10
+idna==3.11
     # via
     #   requests
     #   yarl
-iniconfig==2.1.0
+iniconfig==2.3.0
     # via pytest
-jsonschema-rs==0.33.0
+jsonschema-rs==0.37.1
     # via fourcipp
 kiwisolver==1.4.9
     # via matplotlib
@@ -60,7 +60,7 @@ loguru==0.7.3
     #   lnmmeshio
 markdown-it-py==4.0.0
     # via rich
-matplotlib==3.10.6
+matplotlib==3.10.7
     # via
     #   pyvista
     #   vtk
@@ -70,21 +70,21 @@ meshio==5.3.5
     # via lnmmeshio
 more-itertools==10.8.0
     # via trame-server
-msgpack==1.1.1
+msgpack==1.1.2
     # via wslink
-multidict==6.6.4
+multidict==6.7.0
     # via
     #   aiohttp
     #   yarl
-narwhals==2.5.0
+narwhals==2.12.0
     # via plotly
-netcdf4==1.7.2
+netcdf4==1.7.3
     # via -r requirements.in
 nodeenv==1.9.1
     # via pre-commit
-numexpr==2.13.0
+numexpr==2.14.1
     # via -r requirements.in
-numpy==2.3.3
+numpy==2.3.5
     # via
     #   -r requirements.in
     #   cftime
@@ -104,27 +104,27 @@ packaging==25.0
     #   plotly
     #   pooch
     #   pytest
-pandas==2.3.2
+pandas==2.3.3
     # via -r requirements.in
-pillow==11.3.0
+pillow==12.0.0
     # via
     #   matplotlib
     #   pyvista
-platformdirs==4.4.0
+platformdirs==4.5.0
     # via
     #   pooch
     #   virtualenv
-plotly==6.3.0
+plotly==6.5.0
     # via
     #   -r requirements.in
     #   trame-plotly
 pluggy==1.6.0
     # via pytest
 pooch==1.8.2
     # via pyvista
-pre-commit==4.3.0
+pre-commit==4.5.0
     # via -r requirements.in
-propcache==0.3.2
+propcache==0.4.1
     # via
     #   aiohttp
     #   yarl
@@ -134,7 +134,7 @@ pygments==2.19.2
     #   rich
 pyparsing==3.2.5
     # via matplotlib
-pytest==8.4.2
+pytest==9.0.1
     # via -r requirements.in
 python-dateutil==2.9.0.post0
     # via
@@ -144,30 +144,30 @@ python-utils==3.9.1
     # via lnmmeshio
 pytz==2025.2
     # via pandas
-pyvista==0.46.3
+pyvista==0.46.4
     # via -r requirements.in
-pyyaml==6.0.2
+pyyaml==6.0.3
     # via
     #   lnmmeshio
     #   pre-commit
     #   trame
-rapidyaml==0.9.0
+rapidyaml==0.10.0
     # via fourcipp
-regex==2025.9.18
+regex==2025.11.3
     # via fourcipp
 requests==2.32.5
     # via pooch
-rich==14.1.0
+rich==14.2.0
     # via meshio
-scooby==0.10.2
+scooby==0.11.0
     # via pyvista
 six==1.17.0
     # via python-dateutil
 tqdm==4.66.5
     # via lnmmeshio
 trame==3.12.0
     # via -r requirements.in
-trame-client==3.10.4
+trame-client==3.11.2
     # via
     #   trame
     #   trame-components
@@ -182,11 +182,11 @@ trame-components==2.5.0
     # via -r requirements.in
 trame-plotly==3.1.0
     # via -r requirements.in
-trame-server==3.6.1
+trame-server==3.8.1
     # via trame
-trame-vtk==2.9.1
+trame-vtk==2.10.0
     # via -r requirements.in
-trame-vuetify==3.0.3
+trame-vuetify==3.1.0
     # via -r requirements.in
 typing-extensions==4.15.0
     # via
@@ -197,15 +197,15 @@ tzdata==2025.2
     # via pandas
 urllib3==2.5.0
     # via requests
-virtualenv==20.34.0
+virtualenv==20.35.4
     # via pre-commit
 vtk==9.4.2
     # via
     #   -r requirements.in
     #   pyvista
-wslink==2.4.0
+wslink==2.5.0
     # via
     #   trame
     #   trame-server
-yarl==1.20.1
+yarl==1.22.0
     # via aiohttp

src/fourc_webviewer/fourc_webserver.py

@@ -9,9 +9,9 @@
 
 import numpy as np
 import pyvista as pv
-import yaml
 from fourcipp import CONFIG
 from fourcipp.fourc_input import FourCInput, ValidationError
+from loguru import logger
 from trame.app import get_server
 from trame.decorators import TrameApp, change, controller
 
@@ -30,18 +30,16 @@
 from fourc_webviewer.python_utils import (
     convert_string2number,
     dict_leaves_to_number_if_schema,
-    dict_number_leaves_to_string,
     find_value_recursively,
     parse_validation_error_text,
-    smart_string2number_cast,
 )
 from fourc_webviewer.read_geometry_from_file import (
     FourCGeometry,
 )
 
 # Global variable
 # factor which scales the spheres used to represent nodal design conditions and result descriptions with respect to the problem length scale
-PV_SPHERE_FRAC_SCALE = 1.0 / 45.0
+PV_SPHERE_FRAC_SCALE = 1.0 / 75.0
 
 # always set pyvista to plot off screen with Trame
 pv.OFF_SCREEN = True
@@ -124,6 +122,7 @@ def __init__(
         fourc_geometry = FourCGeometry(
             fourc_yaml_file=fourc_yaml_file,
             temp_dir=Path(self._server_vars["temp_dir_object"].name),
+            first_render=True,
         )
         self.state.vtu_path = fourc_geometry.vtu_file_path
 
@@ -274,8 +273,10 @@ def init_pyvista_render_objects(self):
 
         self._server_vars["render_window"].clear_actors()
 
+        # read problem mesh
         problem_mesh = pv.read(self.state.vtu_path)
-        # get problem mesh
+
+        # save problem mesh as actor
         self._actors["problem_mesh"] = self._server_vars["render_window"].add_mesh(
             problem_mesh, color="bisque", opacity=0.2, render=False
         )
@@ -285,6 +286,7 @@ def init_pyvista_render_objects(self):
         for material in self.state.materials_section.keys():
             # get meshes of materials
             master_mat_ind = self.determine_master_mat_ind_for_material(material)
+
             self._actors["material_meshes"][material] = self._server_vars[
                 "render_window"
             ].add_mesh(
@@ -305,11 +307,11 @@ def init_pyvista_render_objects(self):
         self._actors["dc_geometry_entities"] = {}
         # get nodes of the selected condition geometries + entities
         for dc_entity in all_dc_entities:
-            points = problem_mesh.threshold(
-                value=1.0,
-                scalars=f"d{dc_entity['geometry_type'].lower()}{dc_entity['entity'].replace('E', '')}",
-                preference="point",
-            ).points
+            # get mesh points associated with design condition
+            condition_array_name = f"d{dc_entity['geometry_type'].lower()}{dc_entity['entity'].replace('E', '')}"
+            points = problem_mesh.points[
+                np.where(problem_mesh.point_data[condition_array_name] == 1)[0], :
+            ]
 
             if points.size:
                 pts = pv.PolyData(points)
@@ -449,7 +451,7 @@ def init_general_sections_state_and_server_vars(self):
         ].sections.items():
             if (
                 not any(substr in section_name for substr in substr_to_exclude)
-                and not section_name in sect_to_exclude
+                and section_name not in sect_to_exclude
             ):  # account for sections to be excluded as defined above
                 # check if the current section is "SOLVER<number>"
                 if re.match("^SOLVER [0-9]+", section_name):  # yes
@@ -898,7 +900,9 @@ def init_funct_state_and_server_vars(self):
 
                 else:
                     # warning that this function item is not known
-                    print(f"Unknown function item {item_data} for funct {funct_name}!")
+                    logger.warning(
+                        f"Unknown function item {item_data} for funct {funct_name}!"
+                    )
 
                     # we don't enable visualization
                     item_data["VISUALIZATION"] = False
@@ -1175,11 +1179,6 @@ def change_selected_material(self, selected_material, **kwargs):
         # we need to select the material region based on the newly selected
         # material (if we are not in an initial rendering scenario)
         if self._server_vars["render_count"]["change_selected_material"] > 0:
-            # first get the master material id
-            master_mat_id = self.determine_master_mat_ind_for_material(
-                selected_material
-            )
-
             # update plotter / render objects
             self.update_pyvista_render_objects()
 

src/fourc_webviewer/input_file_utils/fourc_yaml_file_visualization.py

@@ -8,6 +8,7 @@
 import numexpr as ne
 import numpy as np
 import plotly.express as px
+from loguru import logger
 
 from fourc_webviewer.input_file_utils.io_utils import (
     get_variable_data_by_name_in_funct_item,
@@ -261,6 +262,8 @@ def construct_funct_string_from_variable_data(
 
         case _:
             # warning that this variable type is not yet supported for visualization
-            print(f"Variable with {variable_data} not supported for visualization!")
+            logger.warning(
+                f"Variable with {variable_data} not supported for visualization!"
+            )
 
     return funct_string

src/fourc_webviewer/input_file_utils/io_utils.py

@@ -7,6 +7,7 @@
 from pathlib import Path
 
 from fourcipp.fourc_input import FourCInput
+from loguru import logger
 
 from fourc_webviewer.python_utils import flatten_list
 
@@ -39,7 +40,7 @@ def read_fourc_yaml_file(fourc_yaml_file):
         # validate 4C yaml file
         fourc_yaml_content.validate()
     except Exception as exc:
-        print(exc)  # currently, we throw the exception as terminal output
+        logger.error(exc)  # currently, we throw the exception as terminal output
         return (FourCInput({}), [], 0, 0, False)
 
     with open(fourc_yaml_file, "r") as input_file:
@@ -78,7 +79,7 @@ def write_fourc_yaml_file(fourc_yaml_content, new_fourc_yaml_file):
     try:
         fourc_yaml_content.validate()
     except Exception as exc:
-        print(exc)  # currently, we throw the exception as terminal output
+        logger.error(exc)  # currently, we throw the exception as terminal output
         return False
 
     # check if the output file suffix is supported
@@ -251,6 +252,11 @@ def mat_specifiers():
         "VISCOPLAST_LAW_ID",
         "FIBER_READER_ID",
         "STR_TENS_ID",
+        "MATIDSCONST",
+        "MATIDMIXTURERULE",
+        "GROWTH_STRATEGY",
+        "FIBER_MATERIAL_ID",
+        "PRESTRESS_STRATEGY",
     ]