From e3086c43c33475e4df8613e67df28ae8b0fc9f95 Mon Sep 17 00:00:00 2001
From: Paulo Henrique Junqueira Amorim <paulojamorim@gmail.com>
Date: Mon, 23 Sep 2024 23:37:30 -0300
Subject: [PATCH] Command line for automatic export of skull and implant by
 command line. (#850)

---
 app.py                     | 35 ++++++++++++++++++++++--
 invesalius/data/slice_.py  |  1 +
 invesalius/data/surface.py | 56 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 90 insertions(+), 2 deletions(-)

diff --git a/app.py b/app.py
index 0b22ba047..33db1413a 100644
--- a/app.py
+++ b/app.py
@@ -361,7 +361,7 @@ def use_cmd_optargs(args):
             Publisher.sendMessage("Save project", filepath=os.path.abspath(args.save))
             exit(0)
 
-        check_for_segmentation(args)
+        check_for_cranioplasty(args)
         check_for_export(args)
 
         return True
@@ -411,10 +411,41 @@ def use_cmd_optargs(args):
     return False
 
 
-def check_for_segmentation(args):
+def check_for_cranioplasty(args):
+    import invesalius.constants as const
+    from invesalius.i18n import tr as _
+
+    surface_options = {
+        "method": {
+            "algorithm": "Default",
+            "options": {},
+        },
+        "options": {
+            "index": 0,
+            "name": "",
+            "quality": _("Optimal *"),
+            "fill": False,
+            "keep_largest": False,
+            "overwrite": False,
+        },
+    }
+
     if args.cranioplasty:
+        from invesalius.data import slice_
+        from invesalius.project import Project
+
+        # create cranium mask
+        Publisher.sendMessage("Update threshold limits", threshold_range=(226, 3071))
+        Publisher.sendMessage("Appy threshold all slices")
+
+        # create implant mask
         Publisher.sendMessage("Create implant for cranioplasty")
 
+        # convert masks to surfaces and exports them.
+        Publisher.sendMessage(
+            "Export all surfaces separately", folder="./", filetype=const.FILETYPE_STL
+        )
+
 
 def sanitize(text):
     text = str(text).strip().replace(" ", "_")
diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py
index bcf9fa4ea..eeea274ef 100644
--- a/invesalius/data/slice_.py
+++ b/invesalius/data/slice_.py
@@ -254,6 +254,7 @@ def __bind_events(self) -> None:
         Publisher.subscribe(self._fill_holes_auto, "Fill holes automatically")
 
         Publisher.subscribe(self._set_interpolation_method, "Set interpolation method")
+        Publisher.subscribe(self.do_threshold_to_all_slices, "Appy threshold all slices")
 
     def GetMaxSliceNumber(self, orientation: str) -> int:
         shape: Tuple[int, int, int] = self.matrix.shape
diff --git a/invesalius/data/surface.py b/invesalius/data/surface.py
index a3670ff52..d6a0ec7f7 100644
--- a/invesalius/data/surface.py
+++ b/invesalius/data/surface.py
@@ -228,6 +228,7 @@ def __bind_events(self):
         Publisher.subscribe(self.UpdateConvertToInvFlag, "Update convert_to_inv flag")
 
         Publisher.subscribe(self.CreateSurfaceFromPolydata, "Create surface from polydata")
+        Publisher.subscribe(self.export_all_surfaces_separately, "Export all surfaces separately")
 
     def OnDuplicate(self, surface_indexes):
         proj = prj.Project()
@@ -1206,6 +1207,61 @@ def OnExportSurface(self, filename, filetype, convert_to_world=False):
                     dlg.Destroy()
                 os.remove(temp_file)
 
+    def export_all_surfaces_separately(self, folder, filetype):
+        import invesalius.data.slice_ as slc
+
+        if filetype in (
+            const.FILETYPE_STL,
+            const.FILETYPE_VTP,
+            const.FILETYPE_PLY,
+            const.FILETYPE_STL_ASCII,
+        ):
+            proj = prj.Project()
+
+            for index in list(proj.mask_dict.keys()):
+                if index == 1:
+                    algorithm = "Context aware smoothing"
+                else:
+                    algorithm = "Default"
+                surface_parameters = {
+                    "method": {
+                        "algorithm": algorithm,
+                        "options": {},
+                    },
+                    "options": {
+                        "index": index,
+                        "name": "",
+                        "quality": _("Optimal *"),
+                        "fill": False,
+                        "keep_largest": True,
+                        "overwrite": False,
+                    },
+                }
+
+                mask = proj.mask_dict[index]
+                print(mask.matrix.min(), mask.matrix.max(), mask.name)
+                slice_ = slc.Slice()
+
+                Publisher.sendMessage(
+                    "Create surface",
+                    slice_=slice_,
+                    mask=mask,
+                    surface_parameters=surface_parameters,
+                )
+
+            # hide all surfaces
+            for index in proj.surface_dict:
+                proj.surface_dict[index].is_shown = False
+
+            # Displays one surface at a time and export
+            for index in proj.surface_dict.keys():
+                print(proj.surface_dict[index].name)
+                proj.surface_dict[index].is_shown = True
+                self._export_surface(
+                    os.path.join(folder, str(index) + ".stl"), const.FILETYPE_STL, False
+                )
+                proj.surface_dict[index].is_shown = False
+
     def _export_surface(self, filename, filetype, convert_to_world):
         if filetype in (
             const.FILETYPE_STL,