fix: bug fix

.gitignore

@@ -129,4 +129,6 @@ pythonlib*
 
 blendcache_*
 
-*.ipynb
+*.ipynb
+
+.secrets

bioxelnodes/convert.py

@@ -10,6 +10,7 @@ class ConvertToMesh(bpy.types.Operator):
 
     def execute(self, context):
         bioxels_objs = []
+
         for obj in bpy.context.selected_objects:
             bioxels_obj = get_bioxels_obj(obj)
             if bioxels_obj:

bioxelnodes/external_package/package.py

@@ -42,15 +42,13 @@ class InstallationError(Exception):
 class PackageInstaller():
     def __init__(
         self,
+        log_dir: str,
+        requirements_dir: str,
         pypi_mirror_provider='Default',
-        log_dir: str = None,
-        requirements_dir: str = None
     ) -> None:
         self.pypi_mirror_provider = pypi_mirror_provider
-        self.log_path: Path = Path(log_dir) if log_dir else \
+        self.log_path: Path = Path(log_dir)
-            Path(Path.home(), '.externalpackage', 'logs')
+        self.requirements_path: Path = Path(requirements_dir)
-        self.requirements_path: Path = Path(requirements_dir) if requirements_dir else \
-            Path(__file__).parent
 
     def start_logging(self, logfile_name: str = 'side-packages-install') -> logging.Logger:
         """
@@ -233,7 +231,7 @@ class PackageInstaller():
         """
 
         # path to python.exe
-        python_exe = Path(sys.executable).resolve()
+        python_exe = Path(sys.executable).resolve().as_posix()
 
         # build the command list
         cmd_list = [python_exe] + cmd_list
@@ -293,12 +291,11 @@ class PackageInstaller():
             raise ValueError("Package name must be provided.")
 
         print(f"Installing {package}...")
-        print(f"Using PyPI mirror:\
+        print(f"Using PyPI mirror: {self.pypi_mirror_provider}")
-            {self.pypi_mirror_provider} {self.pypi_mirror_url}")
 
         self.run_python(["-m", "ensurepip"]),
         self.run_python(["-m", "pip", "install", "--upgrade", "pip"])
-        result = self.run_python(["-m", "pip", "install", package])
+        result = self.run_python(["-m", "pip", "install", package, "--user"])
 
         return result
 
@@ -348,7 +345,7 @@ class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
     bl_idname = 'externalpackage.install_package'
     bl_label = 'Install Given Python Package'
     bl_options = {'REGISTER', 'INTERNAL'}
-    
+
     package: bpy.props.StringProperty(
         name='Python Package',
         description='Python Package to Install'
@@ -384,7 +381,9 @@ class EXTERNALPACKAGE_OT_Install_Package(bpy.types.Operator):
         else:
             self.report(
                 {'ERROR'},
-                f"Error installing package. Please check the log files in \
+                f"""
-                    '{preferences.log_dir}'."
+Error installing package. Please check the log files
+in {preferences.log_dir}.
+                """
             )
         return {'FINISHED'}

bioxelnodes/external_package/preferences.py

@@ -14,13 +14,13 @@ class ExternalPackagePreferences():
     requirements_dir: bpy.props.StringProperty(
         name="requirements.txt Directory",
         subtype='DIR_PATH',
-        default=''
+        default=Path(__file__).parent.as_posix()
     )  # type: ignore
 
     log_dir: bpy.props.StringProperty(
         name="Python Log Directory",
         subtype='DIR_PATH',
-        default=''
+        default=Path(Path.home(), '.externalpackage', 'logs').as_posix()
     )  # type: ignore
 
     pypi_mirror_provider: bpy.props.StringProperty(
@@ -40,6 +40,7 @@ class ExternalPackagePreferences():
         row_import = col_main.row()
         row_import.prop(self, 'pypi_mirror_provider', text='Set PyPI Mirror')
 
+        
         installer = PackageInstaller(
             pypi_mirror_provider=self.pypi_mirror_provider,
             log_dir=self.log_dir,

bioxelnodes/io.py

@@ -6,12 +6,27 @@ import numpy as np
 from pathlib import Path
 from uuid import uuid4
 import mathutils
-from .utils import calc_bbox_verts, get_bioxels_obj, show_message
+from .utils import calc_bbox_verts, extract_last_number, get_bioxels_obj, show_message
 from .nodes import custom_nodes
 
 SUPPORT_EXTS = ['.dcm', '.tif', '.tiff', '.png', '.bmp']
 
 
+def get_data_files(filepath: str):
+    file_path = Path(filepath).resolve()
+    suffix = file_path.suffix
+
+    files = list(file_path.parent.iterdir())
+    files = [f for f in files if f.is_file() and f.suffix == suffix]
+
+    def last_number(file: Path):
+        return extract_last_number(file.stem)
+
+    files.sort(key=last_number)
+    files = [f.as_posix() for f in files]
+    return files
+
+
 def on_orig_spacing_changed(self, context):
     if self.auto:
         self.auto = False
@@ -122,12 +137,8 @@ class ImportDICOMDialog(bpy.types.Operator):
             return {'CANCELLED'}
 
         file_path = Path(self.filepath).resolve()
-        name = file_path.parent.stem
+        name = file_path.parent.name
-        suffix = file_path.suffix
+        files = get_data_files(self.filepath)
-
-        files = list(file_path.parent.iterdir())
-        files = [f.as_posix()
-                 for f in files if f.is_file() and f.suffix == suffix]
 
         import SimpleITK as sitk
         image = sitk.ReadImage(files)
@@ -174,7 +185,7 @@ class ImportDICOMDialog(bpy.types.Operator):
         image_origin = image.GetOrigin()
         bioxels_scale = float(self.bioxels_scale)
         bioxel_size *= bioxels_scale
-        bioxel_origin = (
+        bioxels_origin = (
             image_origin[0] * bioxels_scale,
             image_origin[1] * bioxels_scale,
             image_origin[2] * bioxels_scale,
@@ -248,7 +259,7 @@ class ImportDICOMDialog(bpy.types.Operator):
         ).to_4x4()
 
         mat_loc = mathutils.Matrix.Translation(
-            mathutils.Vector(bioxel_origin))
+            mathutils.Vector(bioxels_origin))
         mat_sca = mathutils.Matrix.Scale(bioxel_size, 4)
         mat_rot = mathutils.Matrix(
             np.array(direction).reshape((3, 3))
@@ -269,10 +280,12 @@ class ImportDICOMDialog(bpy.types.Operator):
         bioxels_obj['value_max'] = value_max
         bioxels_obj['value_min'] = value_min
         bioxels_obj['value_offset'] = value_offset
+        bioxels_obj['image_origin'] = mathutils.Vector(
+            bioxels_origin) / bioxel_size
+        bioxels_obj['bioxel_size'] = bioxel_size
         bioxels_obj['bioxels_shape'] = bioxels_shape
         bioxels_obj['bioxels_size'] = bioxels_size
-        bioxels_obj['bioxel_size'] = bioxel_size
+        bioxels_obj['bioxels_origin'] = bioxels_origin
-        bioxels_obj['bioxel_origin'] = bioxel_origin
         bioxels_obj['bioxels_values'] = True
 
         bpy.ops.node.new_geometry_nodes_modifier()
@@ -284,7 +297,7 @@ class ImportDICOMDialog(bpy.types.Operator):
         )
         container_obj = bpy.context.active_object
 
-        bbox_verts = calc_bbox_verts(bioxel_origin, bioxels_size)
+        bbox_verts = calc_bbox_verts(bioxels_origin, bioxels_size)
         for index, vert in enumerate(container_obj.data.vertices):
             vert.co = bbox_verts[index]
 
@@ -353,13 +366,7 @@ class ReadDICOM(bpy.types.Operator):
     )  # type: ignore
 
     def execute(self, context):
-
+        files = get_data_files(self.filepath)
-        file_path = Path(self.filepath).resolve()
-        suffix = file_path.suffix
-
-        files = list(file_path.parent.iterdir())
-        files = [f.as_posix()
-                 for f in files if f.is_file() and f.suffix == suffix]
 
         import SimpleITK as sitk
         image = sitk.ReadImage(files)

bioxelnodes/nodes.py

@@ -1,4 +1,5 @@
 
+from pathlib import Path
 from .custom_nodes import CustomNodes
 import bpy
 
@@ -83,7 +84,7 @@ MENU_ITEMS = [
                 'icon': 'EMPTY_DATA',
                 'node_type': 'BioxelNodes_LPS-Slicer',
                 'node_description': '',
-                'node_callback': add_driver_to_node_factory("origin", "Origin")
+                'node_callback': add_driver_to_node_factory("image_origin", "Origin")
             },
             {
                 'label': 'Axis Slicer',
@@ -103,7 +104,7 @@ MENU_ITEMS = [
 
 custom_nodes = CustomNodes(
     menu_items=MENU_ITEMS,
-    nodes_file="assets/Nodes.blend",
+    nodes_file=Path(__file__).parent/"assets/Nodes.blend",
     root_label='BioxelNodes',
     root_icon="FILE_VOLUME",
 )

bioxelnodes/utils.py

@@ -1,13 +1,15 @@
 import bpy
 import mathutils
 
-def show_message(message = "", title = "Message Box", icon = 'INFO'):
+
+def show_message(message="", title="Message Box", icon='INFO'):
 
     def draw(self, context):
         self.layout.label(text=message)
 
-    bpy.context.window_manager.popup_menu(draw, title = title, icon = icon)
+    bpy.context.window_manager.popup_menu(draw, title=title, icon=icon)
-    
+
+
 def calc_bbox_verts(origin, size):
     bbox_origin = mathutils.Vector(
         (-origin[0], -origin[2], -origin[1]))
@@ -76,6 +78,28 @@ def get_bioxels_obj(current_obj):
     return bioxels_obj
 
 
+def extract_last_number(text):
+    # Initialize an empty string to store the digits
+    digits = ""
+
+    # Iterate through the characters in reverse order
+    started = False
+    for char in text[::-1]:
+        if char.isdigit():
+            started = True
+            # If the character is a digit, add it to the digits string
+            digits += char
+        else:
+            if started:
+                # If a non-digit character is encountered, stop the loop
+                break
+
+    # Reverse the digits string to get the correct order
+    last_number = digits[::-1]
+
+    return int(last_number)
+
+
 def add_driver(target_prop, var_sources, expression):
 
     driver = target_prop.driver_add("default_value")