Enable Exodus geometry support

- Added Exodus support for the webviewer:
hereby, the webviewer accounts for multiple sections
ending with "GEOMETRY" for different fields -
all element blocks
are also taken into account when enhancing the
discretization. As restricted by 4C, we only allow for
a single file in all geometry sections.
- Removed these geometry sections from the general
sections within the webviewer, since these are not meant to be
visualized.
- Absolute paths for the exodus files are necessary
due to VFileInput not knowing the local path of the
file.

Author: dragos-ana

src/fourc_webviewer/fourc_webserver.py

@@ -10,13 +10,13 @@
 import numpy as np
 import pyvista as pv
 from fourcipp import CONFIG
+from fourcipp.fourc_input import FourCInput
 from trame.app import get_server
 from trame.decorators import TrameApp, change, controller
 
 import fourc_webviewer.pyvista_render as pv_render
 from fourc_webviewer.gui_utils import create_gui
 from fourc_webviewer.input_file_utils.fourc_yaml_file_visualization import (
-    convert_to_vtu,
     function_plot_figure,
 )
 from fourc_webviewer.input_file_utils.io_utils import (
@@ -26,6 +26,10 @@
     write_fourc_yaml_file,
 )
 from fourc_webviewer.python_utils import convert_string2number, find_value_recursively
+from fourc_webviewer.read_geometry_from_file import (
+    FourCGeometry,
+)
+
 
 # always set pyvista to plot off screen with Trame
 pv.OFF_SCREEN = True
@@ -102,10 +106,12 @@ def __init__(
         self.init_state_and_server_vars()
 
         # convert file to vtu and create dedicated render objects
-        self.state.vtu_path = convert_to_vtu(
-            fourc_yaml_file,
-            Path(self._server_vars["temp_dir_object"].name),
+        fourc_geometry = FourCGeometry(
+            fourc_yaml_file=fourc_yaml_file,
+            temp_dir=Path(self._server_vars["temp_dir_object"].name),
         )
+        self.state.vtu_path = fourc_geometry.vtu_file_path
+
         if self.state.vtu_path == "":
             self.state.read_in_status = self.state.all_read_in_statuses[
                 "vtu_conversion_error"
@@ -258,15 +264,15 @@ def update_pyvista_render_objects(self, init_rendering=False):
         )
 
         # get coords of node with prescribed result description
-        self._server_vars["pv_selected_result_description_node_coords"] = (
-            self._server_vars["pv_mesh"].points[
-                self.state.result_description_section[
-                    self.state.selected_result_description_id
-                ]["PARAMETERS"]["NODE"]
-                - 1,
-                :,
-            ]
-        )
+        self._server_vars[
+            "pv_selected_result_description_node_coords"
+        ] = self._server_vars["pv_mesh"].points[
+            self.state.result_description_section[
+                self.state.selected_result_description_id
+            ]["PARAMETERS"]["NODE"]
+            - 1,
+            :,
+        ]
 
         # update plotter / rendering
         pv_render.update_pv_plotter(
@@ -299,7 +305,14 @@ def init_general_sections_state_and_server_vars(self):
         self.state.json_schema = CONFIG.fourc_json_schema
 
         # define substrings of section names to exclude
-        substr_to_exclude = ["DESIGN", "TOPOLOGY", "ELEMENTS", "NODE", "FUNCT"]
+        substr_to_exclude = [
+            "DESIGN",
+            "TOPOLOGY",
+            "ELEMENTS",
+            "NODE",
+            "FUNCT",
+            "GEOMETRY",
+        ]
         # define full section names to exclude
         sect_to_exclude = [
             "MATERIALS",
@@ -337,9 +350,9 @@ def init_general_sections_state_and_server_vars(self):
                         self.state.general_sections[main_section_name] = {}
 
                     # add subsection
-                    self.state.general_sections[main_section_name][section_name] = (
-                        section_data
-                    )
+                    self.state.general_sections[main_section_name][
+                        section_name
+                    ] = section_data
 
     def sync_general_sections_from_state(self):
         """Syncs the server-side general sections based on the current values
@@ -421,9 +434,9 @@ def init_materials_state_and_server_vars(self):
             ):
                 if mat_id in linked_material_indices_item:
                     # add linked material indices
-                    mat_item_val["RELATIONSHIPS"]["LINKED MATERIALS"] = (
-                        linked_material_indices_item
-                    )
+                    mat_item_val["RELATIONSHIPS"][
+                        "LINKED MATERIALS"
+                    ] = linked_material_indices_item
 
                     # add master material index
                     mat_item_val["RELATIONSHIPS"]["MASTER MATERIAL"] = material_indices[
@@ -483,9 +496,9 @@ def sync_materials_sections_from_state(self):
         # write to server-side content
         self._server_vars["fourc_yaml_content"]["MATERIALS"] = new_materials_section
         if new_cloning_material_map_section:
-            self._server_vars["fourc_yaml_content"]["CLONING MATERIAL MAP"] = (
-                new_cloning_material_map_section
-            )
+            self._server_vars["fourc_yaml_content"][
+                "CLONING MATERIAL MAP"
+            ] = new_cloning_material_map_section
 
     def init_design_conditions_state_and_server_vars(self):
         """Initialize the state and server variables for the design condition
@@ -677,9 +690,9 @@ def sync_result_description_section_from_state(self):
             new_result_description_section.append({field: params})
 
         # set result description section on the server
-        self._server_vars["fourc_yaml_content"]["RESULT DESCRIPTION"] = (
-            new_result_description_section
-        )
+        self._server_vars["fourc_yaml_content"][
+            "RESULT DESCRIPTION"
+        ] = new_result_description_section
 
     def init_funct_state_and_server_vars(self):
         """Initialize the state and server variables for the function
@@ -1058,6 +1071,7 @@ def click_convert_button(self, **kwargs):
 
         with open(temp_fourc_yaml_file, "w") as f:
             f.write(self.state.fourc_yaml_file["content"].decode("utf-8"))
+        # copy eventual exodus file as well
 
         if self._server_vars["fourc_yaml_read_in_status"]:
             self.state.read_in_status = self.state.all_read_in_statuses["success"]
@@ -1066,10 +1080,11 @@ def click_convert_button(self, **kwargs):
             self.init_state_and_server_vars()
 
             # convert to vtu
-            self.state.vtu_path = convert_to_vtu(
-                temp_fourc_yaml_file,
-                Path(self._server_vars["temp_dir_object"].name),
+            fourc_geometry = FourCGeometry(
+                fourc_yaml_file=temp_fourc_yaml_file,
+                temp_dir=Path(self._server_vars["temp_dir_object"].name),
             )
+            self.state.vtu_path = fourc_geometry.vtu_file_path
 
             # catch eventual conversion error
             if self.state.vtu_path == "":

src/fourc_webviewer/input_file_utils/fourc_yaml_file_visualization.py

@@ -9,37 +9,6 @@
 import numpy as np
 import plotly.express as px
 
-from fourc_webviewer.input_file_utils.io_utils import (
-    add_fourc_yaml_file_data_to_dis,
-)
-
-
-def convert_to_vtu(fourc_yaml_file_path, temp_dir):
-    """Convert fourc yaml file to vtu.
-
-    Args:
-        fourc_yaml_file_path (str, Path): Path to input file
-        temp_dir (str, Path): Temp directory
-
-    Returns:
-        str: Path to vtu file
-    """
-    # define the vtu_file_path to have the same name as the input file, but the its directory is in './temp_files'
-    vtu_file_path = str(Path(temp_dir) / f"{Path(fourc_yaml_file_path).stem}.vtu")
-
-    # convert yaml file to vtu file and return the path to the vtu file
-    try:
-        dis = lnmmeshio.read(str(fourc_yaml_file_path))
-
-        to_vtu(dis, vtu_file_path)
-    except Exception as exc:  # if file conversion not successful
-        print(
-            exc
-        )  # currently, we throw the lnmmeshio conversion error as terminal output
-        vtu_file_path = ""
-
-    return vtu_file_path
-
 
 def function_plot_figure(state_data):
     """Get function plot figure.
@@ -149,7 +118,7 @@ def funct_using_eval(x, y, z, t):
         # funct_string copy
         funct_string_copy = funct_string
 
-        # replace the defined functions in the funct_string with "np.<def_funct>"
+        # replace the defined functions in the funct_string with "<def_funct>"
         for i in range(len(def_funct)):
             funct_string_copy = funct_string_copy.replace(
                 def_funct[i], f"np.{def_funct[i]}"
@@ -174,25 +143,8 @@ def funct_using_eval(x, y, z, t):
             r"heaviside\((.*?)\)", r"heaviside(\1,0)", funct_string_copy
         )  # usage of raw strings, (.*?) is a non greedy capturing, and \1 replaces the captured value
 
-        return ne.evaluate(funct_string_copy)  # this parses string in as a function
+        return eval(
+            funct_string_copy, {"np": np}, {}
+        )  # this parses string in as a function
 
     return np.frompyfunc(funct_using_eval, 4, 1)
-
-
-def to_vtu(dis, vtu_file: str, override=True):
-    """Discretization to vtu.
-
-    Args:
-        dis (lnmmeshio.Discretization): Discretization object
-        vtu_file (str): Path to vtu file
-        override (bool, optional): Overwrite existing file. Defaults to True
-    """
-    add_fourc_yaml_file_data_to_dis(dis)
-
-    # write case file
-    lnmmeshio.write(
-        vtu_file,
-        dis,
-        file_format="vtu",
-        override=override,
-    )

src/fourc_webviewer/input_file_utils/io_utils.py

@@ -91,51 +91,6 @@ def write_fourc_yaml_file(fourc_yaml_content, new_fourc_yaml_file):
     return True
 
 
-def add_fourc_yaml_file_data_to_dis(dis):
-    """Adds further data contained within the yaml file (e.g. material id) to
-    the discretization from lnmmeshio."""
-    dis.compute_ids(zero_based=False)
-
-    # write node data
-    for n in dis.nodes:
-        # write node id
-        n.data["node-id"] = n.id
-        n.data["node-coords"] = n.coords
-
-        # write fibers
-        for name, f in n.fibers.items():
-            n.data["node-" + name] = f.fiber
-
-        # write dpoints
-        for dp in n.pointnodesets:
-            n.data["dpoint{0}".format(dp.id)] = 1.0
-
-        # write dlines
-        for dl in n.linenodesets:
-            n.data["dline{0}".format(dl.id)] = 1.0
-
-        # write dsurfs
-        for ds in n.surfacenodesets:
-            n.data["dsurf{0}".format(ds.id)] = 1.0
-
-        # write dvols
-        for dv in n.volumenodesets:
-            n.data["dvol{0}".format(dv.id)] = 1.0
-
-    # write element data
-    for elements in dis.elements.values():
-        for ele in elements:
-            ele.data["element-id"] = ele.id
-
-            # write mat
-            if "MAT" in ele.options:
-                ele.data["element-material"] = int(ele.options["MAT"])
-
-            # write fibers
-            for name, f in ele.fibers.items():
-                ele.data["element-" + name] = f.fiber
-
-
 def find_linked_materials(material_id, material_items):
     """Find materials linked with a material number / id recursively based on
     given material specifiers (parameters which refer to other materials). This
@@ -237,7 +192,9 @@ def get_main_and_clustered_section_names(sections_list):
             # append the main section "FUNCTIONS"
             main_sections.append("FUNCTIONS")
 
-            clustered_sections_to_be_added = []  # list of clustered sections to be added
+            clustered_sections_to_be_added = (
+                []
+            )  # list of clustered sections to be added
             # add current element to clustered sections and remove it from sections
             clustered_sections_to_be_added.append(sections.pop(0))
 
@@ -252,7 +209,6 @@ def get_main_and_clustered_section_names(sections_list):
 
             # add the clustered sections
             clustered_sections.append(clustered_sections_to_be_added)
-
         else:  # no
             # check if element already in main sections -> SHOULD NEVER HAPPEN
             if sections[0].split("/")[0] in main_sections:
@@ -359,7 +315,9 @@ def get_master_and_linked_material_indices(materials_section):
     master_mat_indices = [mat_item["MAT"] for mat_item in materials_section]
 
     # check whether some of the master materials are actually related to others, and eliminate them from the master material index list
-    linked_mat_indices = []  # list of linked material indices for each of the "master" materials: [<list of linked materials for "MASTER" 1>, <list of linked materials for "MASTER" 2>,... ]
+    linked_mat_indices = (
+        []
+    )  # list of linked material indices for each of the "master" materials: [<list of linked materials for "MASTER" 1>, <list of linked materials for "MASTER" 2>,... ]
     for master_mat_index in master_mat_indices:
         linked_mat_indices.append(
             find_linked_materials(
@@ -381,9 +339,7 @@ def get_master_and_linked_material_indices(materials_section):
                 del master_mat_indices[next_master_list_ind]
                 del linked_mat_indices[next_master_list_ind]
             # next_master_ind stays the same
-            elif set(
-                linked_mat_indices[curr_master_list_ind]
-            ).issubset(
+            elif set(linked_mat_indices[curr_master_list_ind]).issubset(
                 set(linked_mat_indices[next_master_list_ind])
             ):  # this means that the current element is not truly a master -> has to be eliminated and we also break out of the for-loop
                 del master_mat_indices[curr_master_list_ind]