feat(3D): export quantitative data directly from meshes

Author: quasiTriestino

PyReconstruct/modules/backend/volume/export_volumes.py

@@ -1,7 +1,7 @@
 """Export 3D objects."""
 
 from pathlib import Path
-from typing import List
+from typing import List, Union
 
 import numpy as np
 import trimesh
@@ -24,47 +24,13 @@ def export3DObjects(series: Series, obj_names : list, output_dir : str, export_t
             void
     """
 
+    ## Collect 3D objects
+    
     obj_data = {}
 
     for obj_name in obj_names:
 
-        mode = series.getAttr(obj_name, "3D_mode")
-            
-        if mode == "surface":
-            obj_data[obj_name] = Surface(obj_name, series)
-            
-        elif mode == "spheres":
-            obj_data[obj_name] = Spheres(obj_name, series)
-            
-        elif mode == "contours":
-            obj_data[obj_name] = Contours(obj_name, series)
-
-    for snum, section in series.enumerateSections(show_progress=False):
-
-        # # Assume somewhat uniform section thickness
-        # tform = section.tform
-
-        for obj_name in obj_names:
-
-            if obj_name not in section.contours:
-
-                continue
-
-            ## Get objects alignment
-            obj_alignment = series.getAttr(obj_name, "alignment")
-
-            if not obj_alignment:
-                
-                tform = section.tform
-            
-            else:
-
-                tform = section.tforms[obj_alignment]
-            
-            for trace in section.contours[obj_name]:
-
-                ## Collect all points if generating full surface
-                obj_data[obj_name].addTrace(trace, snum, tform)
+        obj_data[obj_name] = get_3D_mesh(series, obj_name)
 
     ## Iterate through objects and export 3D meshes
 
@@ -83,7 +49,93 @@ def export3DObjects(series: Series, obj_names : list, output_dir : str, export_t
 
     if notify_user:
 
-        notify(f"Object(s) exported to directory:\n\n{output_directory.absolute()}\n")
+        notify(f"Object(s) exported to directory:\n\n{Path(output_directory).absolute()}\n")
+
+
+def export3DData(series: Series, obj_names: list, output_fp: str, notify_user: bool=True) -> None:
+    """Export quantitative data from meshes."""
+
+    sep = ","
+    csv_str = f"Series{sep}Name{sep}MeshType{sep}SurfaceArea{sep}Volume\n"
+    series_code = series.code
+
+    errors = {}
+
+    for obj in obj_names:
+
+        try:
+
+            obj_data = get_3D_mesh(series, obj)
+            obj_type = type(obj_data).__name__.lower()
+            tm = obj_data.generateTrimesh()
+
+            surface_area = round(tm.area, 5)
+            volume = round(tm.volume, 5)
+
+            csv_str += f"{series_code}{sep}{obj}{sep}{obj_type}{sep}{surface_area}{sep}{volume}\n"
+
+        except Exception as e:
+
+            errors[obj] = e
+
+    if not errors:
+
+        with open(output_fp, "w") as fp:
+            fp.write(csv_str)
+
+        if notify_user:
+            notify(f"Data exported to:\n\n{Path(output_fp).absolute()}\n")
+
+    if errors:
+
+        print(errors)
+        notify("There were errors exporting data from some or all of the objects. See console.")
+
+        
+def get_3D_mesh(series: Series, obj_name: str) -> Union[Surface, Spheres, Contours]:
+    """Get mesh for an object."""
+
+    ## Create initial 3D obj
+
+    mode = series.getAttr(obj_name, "3D_mode")
+            
+    if mode == "surface":
+        obj_data = Surface(obj_name, series)
+            
+    elif mode == "spheres":
+        obj_data = Spheres(obj_name, series)
+            
+    elif mode == "contours":
+        obj_data = Contours(obj_name, series)
+
+    ## Iterate through sections and collect data
+
+    for snum, section in series.enumerateSections(show_progress=False):
+
+        ## Assume somewhat uniform section thickness
+        # tform = section.tform
+
+        if obj_name not in section.contours:
+
+            continue
+
+        ## Get alignment
+        obj_alignment = series.getAttr(obj_name, "alignment")
+
+        if not obj_alignment:
+
+            tform = section.tform
+
+        else:
+
+            tform = section.tforms[obj_alignment]
+
+        for trace in section.contours[obj_name]:
+
+            ## Collect all points if generating full surface
+            obj_data.addTrace(trace, snum, tform)
+    
+    return obj_data
 
 
 def convert_vedo_to_tm(obj) -> trimesh.Trimesh:

PyReconstruct/modules/backend/volume/objects_3D.py

@@ -59,6 +59,7 @@ def addToExtremes(self, x, y, s):
             if s < self.extremes[4]: self.extremes[4] = s
             if s > self.extremes[5]: self.extremes[5] = s
 
+
 class Surface(Object3D):
 
     def __init__(self, *args):
@@ -257,6 +258,7 @@ def generate3D(self):
 
         return mesh_data
 
+
 class Contours(Object3D):
 
     def __init__(self, *args):

PyReconstruct/modules/datatypes/series_data.py

@@ -1,4 +1,5 @@
 """Collect data to pass to table manager."""
+
 from typing import Union
 
 from PyReconstruct.modules.calc import lineDistance, area
@@ -345,9 +346,16 @@ def getVolume(self, obj_name : str) -> float:
 
             for trace_data in trace_list:
                 v += trace_data.getArea() * self.data["sections"][snum]["thickness"]
-                
+        
         return v
 
+    def getSurfaceArea(self, obj_name: str) -> float:
+        """Get the surface area of an object."""
+
+        from PyReconstruct.modules.backend.volume.export_volumes import get_3D_mesh
+
+        pass
+
     def getConfiguration(self, obj_name: str) -> Union[str, None]:
         """Get the configuration of the object.
 

PyReconstruct/modules/gui/main/context_menu_list.py

@@ -121,7 +121,7 @@ def get_context_menu_list_obj(self):
                 ("removeobj3D_act", "Remove from scene", "", self.remove3D),
                 {
                     "attr_name": "exportobj3D",
-                    "text": "Export",
+                    "text": "Export meshes",
                     "opts":
                     [
                         ("export3D_act", "Wavefront (.obj)", "", lambda : self.exportAs3D("obj")),
@@ -132,6 +132,7 @@ def get_context_menu_list_obj(self):
                     ]
 
                     },
+                ("exportmeshdata", "Export quantitative data", "", self.export3DData),
                 None,
                 ("editobj3D_act", "Edit 3D settings...", "", self.edit3D)
             ]

PyReconstruct/modules/gui/main/field_widget_3_object.py

@@ -311,6 +311,11 @@ def exportAs3D(self, obj_names : list, export_type):
         """Export 3D objects."""
         self.mainwindow.exportAs3D(obj_names, export_type)
 
+    @object_function(update_objects=False, reload_field=False)
+    def export3DData(self, obj_names: list):
+        """Export quantitative data from 3D meshes."""
+        self.mainwindow.export3DData(obj_names)
+        
     @object_function(update_objects=True, reload_field=False)
     def addToGroup(self, obj_names : list, log_event=True):
         """Add objects to a group."""

PyReconstruct/modules/gui/main/main_imports.py

@@ -108,7 +108,8 @@
 )
 
 from PyReconstruct.modules.backend.volume import (
-    export3DObjects
+    export3DObjects,
+    export3DData
 )
 
 from PyReconstruct.modules.backend.imports import (

PyReconstruct/modules/gui/main/main_window.py

@@ -2372,6 +2372,25 @@ def exportAs3D(self, obj_names, export_type, ztraces=False):
             )
         if not export_dir: return
         export3DObjects(self.series, obj_names, export_dir, export_type)
+
+    def export3DData(self, obj_names):
+        """Export quantitative data from meshes."""
+        
+        notify(
+            f"3D surface area and volume measurements depend on the meshing algorithm "
+            f"implemented in PyReconstruct. We recommend verifying proper mesh quality by "
+            f"inspecting objects in the 3D scene before analyzing quantitative data.\n\n"
+            f"Click OK to specificy where to save this data."
+        )
+        
+        self.saveAllData()
+        
+        output_fp = FileDialog.get(
+            "save", self, "Save data as CSV file", "*.csv", "mesh_data.csv"
+        )
+        if not output_fp: return
+
+        export3DData(self.series, obj_names, output_fp)
 
     def toggleCuration(self):
         """Quick shortcut to toggle curation on/off for the tables."""

PyReconstruct/modules/gui/table/object.py

@@ -883,7 +883,7 @@ def exportUserColText(self):
             return
 
         self.series.exportUserColsText(out_fp)
-    
+
     def importUserColText(self):
         """Import user columns from a text file."""
         fp = FileDialog.get(