Merge pull request #36 from SPARC-FAIR-Codeathon/mesh_generation

Mesh generation

src/main.py

@@ -9,3 +9,5 @@
 scaffold.update_mesh_label(original_name="unnamed", new_name="whole_stomach")
 
 scaffold.plot()
+
+scaffold.export("output.stl")

src/sparc_spy/__init__.py

@@ -1,2 +1,2 @@
-from sparc_spy.mesh import Mesh
+from sparc_spy.meshes import Meshes
 from sparc_spy.scaffold import Scaffold

src/sparc_spy/mesh.py → src/sparc_spy/meshes.py

@@ -2,22 +2,27 @@
 import shutil
 import pyvista as pv
 from io import StringIO
+
 
-class Meshes(object):
+class Meshes(pv.MultiBlock): 
     def __init__(self) -> None:
-        self.meshes = pv.MultiBlock()  
+        super().__init__()
 
     def add_mesh(self, label: str, mesh: pv.PolyData): 
-        self.meshes.append(label, mesh) 
+        self.append(label, mesh) 
 
     def export(self, output_filepath: str = "output.stl", base_path='.'):  
-        save_multiblock_stl(self.meshes, output_filepath, base_path) 
+        save_multiblock_stl(self, output_filepath, base_path) 
 
-    def items(self):
-        items = []
-        for key in self.meshes.keys():
-            items.append((key, self.meshes[key]))
-        return items
+    def items(self): 
+        '''  
+        This function should return the label and meshes (pv.PolyData) in the MultiBlock object.
+        ''' 
+        blocks = [] 
+        for name in self.keys(): 
+            blocks.append((name, self[name]))
+
+        return blocks
 
 
 def save_multiblock_stl(multiblock, filename, base_path='.'):

src/sparc_spy/scaffold.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pyvista as pv
 
-from sparc_spy import Mesh
+from sparc_spy import Meshes
 
 
 def populate_metadata(paths):
@@ -83,11 +83,11 @@ def populate_metadata(paths):
 
 
 class Scaffold(object):
-    meshes: Dict
+    meshes: Meshes
 
     def __init__(self, name, derivative_dir: str):
         self.name = name
-        self.meshes = {}
+        self.meshes = Meshes()
         self.metadata = populate_metadata(self.__read_jsons(derivative_dir))
         self.geometry = self.build_scaffold(derivative_dir)
 
@@ -118,7 +118,7 @@ def build_scaffold(self, derivative_dir: str):
                 vertices = vertices.reshape(-1, 3)
 
                 mesh = pv.PolyData(vertices, faces)
-                self.meshes[label] = mesh
+                self.meshes[label] = mesh 
 
     def plot(self):
         pv.global_theme.color_cycler = ["#DA627D", "#33658A", "#86BBD8", "#06969A", "#9A348E"]
@@ -128,19 +128,21 @@ def plot(self):
         pl.add_legend()
         pl.show()
 
-    def export(self, output_filepath: str = "output.vtk"):
-        """Export the scaffold to a .vtk file
+    def export(self, output_filepath: str = "output.stl", base_path="."):
+        """Export the scaffold to a .stl file
 
         Args:
             output_filepath (str, optional): output_filepath (str): Output file
             path to save .vtk file. Defaults to "output.vtk".
-        """
+        """  
+        self.meshes.export(output_filepath, base_path)
+
 
     def get_metadata(self):
         """Show a tabular view of metadata that is important to the user"""
         return
 
-    def add_mesh(self, mesh_name: str, mesh: Mesh):
+    def add_mesh(self, mesh_name: str, mesh: pv.PolyData):
         """Modify self.meshes and add a new mesh to the list.
 
         Args: