Improving Mesh class documentation

.zenodo.json

@@ -0,0 +1,33 @@
+{
+    "creators": [
+        {
+            "orcid": "0000-0003-1876-7042",
+            "affiliation": "Auckland Bioengineering Institute, University of Auckland",
+            "name": "Hoffman, Michael"
+        },
+        {
+            "orcid": "0000-0002-5929-9794",
+            "affiliation": "Auckland Bioengineering Institute, University of Auckland",
+            "name": "Wijenayaka, Savindi"
+        },
+        {
+            "orcid": "0000-0002-4917-7144",
+            "affiliation": "Auckland Bioengineering Institute, University of Auckland",
+            "name": "Malik, Mishaim"
+        },
+        {
+            "orcid": "0000-0003-0175-3488",
+            "affiliation": "Auckland Bioengineering Institute, University of Auckland",
+            "name": "French, Matthew"
+        },
+        {
+            "orcid": "0000-0003-4758-769X",
+            "affiliation": "Auckland Bioengineering Institute, University of Auckland",
+            "name": "Gu, Yun"
+        }
+    ],
+
+    "license": "Apache-2.0",
+
+    "title": "SPARC Python Imager (SPARC-SPy)"
+}

requirements.txt

@@ -4,3 +4,5 @@ libstdcxx-ng==14.1.0
 pandas==2.2.2
 hurry.filesize==0.9
 tabulate==0.9.0
+sparc-me==3.0.0
+numpy==2.0.1

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/meshes.py

@@ -0,0 +1,106 @@
+import os 
+import shutil
+import pyvista as pv
+from io import StringIO
+
+
+class Meshes(pv.MultiBlock): 
+    def __init__(self) -> None: 
+        """ 
+        This class is a subclass of pyvista.MultiBlock. 
+        It is used to store multiple meshes with labels from the scaffold.
+        """
+        super().__init__()
+
+    def add_mesh(self, label: str, mesh: pv.PolyData):  
+        """ 
+        This function adds a mesh to the MultiBlock object. 
+        Args: 
+            label (str): Label of the mesh. 
+            mesh (pv.PolyData): Mesh to be added.  
+        """
+        self.append(label, mesh) 
+
+    def export(self, output_filepath: str = "output.stl", base_path='.'):   
+        """ 
+        This function exports the meshes in the MultiBlock object to a single STL file. 
+        Args: 
+            output_filepath (str): Output file path. 
+            base_path (str): Base path. 
+        """
+        save_multiblock_stl(self, output_filepath, base_path) 
+
+    def items(self): 
+        '''  
+        This function should return the label and meshes (pv.PolyData) in the MultiBlock object. 
+        Returns: 
+            list: List of tuples containing label and mesh.
+        ''' 
+        blocks = [] 
+        for name in self.keys(): 
+            blocks.append((name, self[name]))
+
+        return blocks
+
+
+def save_multiblock_stl(multiblock, filename, base_path='.'): 
+    """ 
+    This function saves the meshes in the MultiBlock object to a single STL file. 
+    Args: 
+        multiblock (MultiBlock): MultiBlock object containing meshes. 
+        filename (str): Output file path. 
+        base_path (str): Base path. 
+    """
+
+    names = multiblock.keys()
+    oname, ext = os.path.splitext(filename)
+    assert ext == '.stl'
+
+    # each individual stl file saved (output_filenames)
+    ofiles = [os.path.join(base_path, f'{oname}_{ii}') + '.stl' for ii in range(len(names))]
+
+    for ii, subpart in enumerate(multiblock):
+        subpart.save(ofiles[ii], binary=False)
+        change_first_line_of_file(ofiles[ii], f'solid {names[ii]}') # basically changes "solid" to "solid <solid_name>"
+
+    # merge files together
+    total_stl = ''
+    for fn in ofiles:
+        f = open(fn)
+        total_stl += f.read()
+        f.close()
+
+    # writes total stl file 
+    total_file_name = os.path.join(base_path, oname + '.stl')
+    with open(total_file_name, 'w') as f:
+        f.write(total_stl)
+
+    # deletes previously written stl files
+    for fn in ofiles:
+        os.remove(fn)
+
+    return
+
+def change_first_line_of_file(filename, new_first_line): 
+    """ 
+    This function changes the first line of a file. 
+    Args: 
+        filename (str): File name. 
+        new_first_line (str): New first line. 
+    """
+
+    fr = open(filename, 'r')
+    first_line = fr.readline()
+    fr.close()
+    first_line_len = len(first_line)
+
+    new_first_line_len = len(new_first_line)
+    spaces_num = first_line_len - new_first_line_len
+    new_first_line = new_first_line + ' '*(spaces_num-1) + '\n'
+    fw = StringIO(new_first_line)
+    fr = open(filename, 'r+')
+    shutil.copyfileobj(fw, fr)
+    fr.close()
+    fw.close()
+    return
+

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"]
@@ -128,26 +128,28 @@ 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".
-        """
+            path to save .stl 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:
             mesh_name (str): User defined name for the mesh
             mesh (Mesh): Mesh containing new experimental data
         """
-        return
+        self.meshes[mesh_name] = mesh
 
     def get_mesh_details(self):
         """List all meshes with their corresponding user defined names. These IDs