install oct2py and jdata from GUI, convert isnormalized properly

__init__.py

@@ -75,9 +75,12 @@
 from .niifile import niifile
 from .nii2mesh import nii2mesh
 from bpy.props import PointerProperty
+from .pkg import InstallOct2py, InstallJData
 
 def register():
     print("Registering BlenderPhotonics")
+    bpy.utils.register_class(InstallOct2py)
+    bpy.utils.register_class(InstallJData)
     bpy.utils.register_class(scene2mesh)
     bpy.utils.register_class(object2surf)
     bpy.utils.register_class(niifile)
@@ -90,6 +93,8 @@ def register():
 
 def unregister():
     print("Unregistering BlenderPhotonics")
+    bpy.utils.unregister_class(InstallOct2py)
+    bpy.utils.unregister_class(InstallJData)
     bpy.utils.unregister_class(scene2mesh)
     bpy.utils.unregister_class(object2surf)
     bpy.utils.unregister_class(niifile)

blender2mesh.py

@@ -23,8 +23,6 @@
 
 import bpy
 import numpy as np
-import jdata as jd
-import os
 from bpy.utils import register_class, unregister_class
 from .utils import *
 
@@ -69,6 +67,9 @@ def description(cls, context, properties):
         return hints[properties.endstep]
 
     def func(self):
+        import jdata as jd
+        import os
+
         outputdir = GetBPWorkFolder();
         if not os.path.isdir(outputdir):
             os.makedirs(outputdir)

mesh2blender.py

@@ -23,8 +23,6 @@
 
 import bpy
 import numpy as np
-import jdata as jd
-import os
 from .utils import *
 
 class mesh2scene(bpy.types.Operator):
@@ -33,6 +31,8 @@ class mesh2scene(bpy.types.Operator):
     bl_idname = 'blenderphotonics.meshtoscene'
 
     def importmesh(self):
+        import jdata as jd
+        import os
         # clear all object
         bpy.ops.object.select_all(action='SELECT')
         bpy.ops.object.delete()

nii2mesh.py

@@ -24,8 +24,6 @@
 
 import bpy
 import numpy as np
-import jdata as jd
-import os
 from .utils import *
 
 g_maxvol=100
@@ -51,6 +49,9 @@ class nii2mesh(bpy.types.Operator):
     method: bpy.props.EnumProperty(name="Mesh extraction method", items = [('auto','auto','auto'),('cgalmesh','cgalmesh','cgalmesh'), ('cgalsurf','cgalsurf','cgalsurf'), ('simplify','simplify','simplify')])
 
     def vol2mesh(self):
+        import jdata as jd
+        import os
+
         # Remove last .jmsh file
         outputdir = GetBPWorkFolder()
         if not os.path.isdir(outputdir):

obj2surf.py

@@ -23,8 +23,6 @@
 import bpy
 from bpy_extras.io_utils import ImportHelper
 import numpy as np
-import jdata as jd
-import os
 from bpy.utils import register_class, unregister_class
 from .utils import *
 
@@ -66,6 +64,9 @@ def description(cls, context, properties):
         return hints[properties.action]
 
     def func(self):
+        import jdata as jd
+        import os
+
         outputdir = GetBPWorkFolder();
         if not os.path.isdir(outputdir):
             os.makedirs(outputdir)

pkg.py

@@ -0,0 +1,31 @@
+import bpy
+import subprocess
+import sys
+import os
+import pathlib
+
+
+class InstallOct2py(bpy.types.Operator):
+    bl_idname = "blenderphotonics.install_oct2py"
+    bl_label = "Install Package"
+    bl_description = "Install Oct2py Python package"
+    bl_options = {"REGISTER", "UNDO"}
+
+    def execute(self, context):
+        # Install Oct2py
+        ADDON_DIR = os.path.join(os.path.abspath(pathlib.Path(__file__).resolve().parent.parent), "modules")
+        subprocess.call([sys.executable, "-m", "pip", "install", "oct2py", "--target=" + ADDON_DIR])
+        return {"FINISHED"}
+
+
+class InstallJData(bpy.types.Operator):
+    bl_idname = "blenderphotonics.install_jdata"
+    bl_label = "Install Package"
+    bl_description = "Install JData package"
+    bl_options = {"REGISTER", "UNDO"}
+
+    def execute(self, context):
+        # Install JData
+        ADDON_DIR = os.path.join(os.path.abspath(pathlib.Path(__file__).resolve().parent.parent), "modules")
+        subprocess.call([sys.executable, "-m", "pip", "install", "jdata", "--target=" + ADDON_DIR])
+        return {"FINISHED"}

runmmc.py

@@ -23,8 +23,6 @@
 
 import bpy
 import numpy as np
-import jdata as jd
-import os
 from .utils import *
 
 g_nphoton=10000
@@ -59,6 +57,9 @@ class runmmc(bpy.types.Operator):
     debuglevel: bpy.props.StringProperty(default=g_debuglevel,name="Debug flag [MCBWDIOXATRPE]")
 
     def preparemmc(self):
+        import jdata as jd
+        import os
+
         ## save optical parameters and source source information
         parameters = [] # mu_a, mu_s, n, g
         cfg = [] # location, direction, photon number, Type,

script/blendermmc.m

@@ -63,7 +63,7 @@ function blendermmc(paramfile, meshfile)
 cfg.tend=param.cfg.tend;
 cfg.tstep=param.cfg.tstep;
 cfg.isreflect=double(param.cfg.isreflect);
-cfg.isnormalized=param.cfg.isnormalized;
+cfg.isnormalized=double(param.cfg.isnormalized);
 cfg.gpuid=param.cfg.gpuid;
 cfg.unitinmm = param.cfg.unitinmm;
 cfg.outputtype=param.cfg.outputtype;

ui.py

@@ -28,6 +28,7 @@
 from .niifile import niifile
 from .nii2mesh import nii2mesh
 from .obj2surf import object2surf
+from .pkg import InstallJData, InstallOct2py
 
 class BlenderPhotonics_UI(bpy.types.Panel):
     bl_label = 'BlenderPhotonics v2022'
@@ -45,6 +46,9 @@ def draw(self, context):
         scene = context.scene
         bp = scene.blender_photonics
         rowengine = layout.row()
+        rowengine.operator(InstallOct2py.bl_idname, text="Install Oct2py", icon='FILE_TICK')
+        rowengine.operator(InstallJData.bl_idname, text="Install JData", icon='FILE_TICK')
+        rowengine = layout.row()
         rowengine.label(text="Backend:")
         rowengine.prop(bp, "backend", expand=True)