From fec580984dd9dc79ada1323a59ca122feec52c23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Pedersen?= <andrped94@gmail.com>
Date: Tue, 31 Oct 2023 15:07:18 +0100
Subject: [PATCH 1/2] Renamed to nifti_to_obj and moved to convert

---
 demo/src/convert.py | 35 +++++++++++++++++++++++++++++++++++
 demo/src/gui.py     |  6 +++---
 demo/src/utils.py   | 34 ----------------------------------
 3 files changed, 38 insertions(+), 37 deletions(-)
 create mode 100644 demo/src/convert.py

diff --git a/demo/src/convert.py b/demo/src/convert.py
new file mode 100644
index 0000000..d4b97da
--- /dev/null
+++ b/demo/src/convert.py
@@ -0,0 +1,35 @@
+import nibabel as nib
+from nibabel.processing import resample_to_output
+from skimage.measure import marching_cubes
+
+
+def nifti_to_obj(path, output="prediction.obj"):
+    # load NIFTI into numpy array
+    image = nib.load(path)
+    resampled = resample_to_output(image, [1, 1, 1], order=1)
+    data = resampled.get_fdata().astype("uint8")
+
+    # Create a material with a red diffuse color (RGB value)
+    red_material = "newmtl RedMaterial\nKd 1 0 0"  # Red diffuse color (RGB)
+
+    # extract surface
+    verts, faces, normals, values = marching_cubes(data, 0)
+    faces += 1
+
+    with open(output, "w") as thefile:
+        # Write the material definition to the OBJ file
+        thefile.write(red_material + "\n")
+
+        for item in verts:
+            # thefile.write('usemtl RedMaterial\n')
+            thefile.write("v {0} {1} {2}\n".format(item[0], item[1], item[2]))
+
+        for item in normals:
+            thefile.write("vn {0} {1} {2}\n".format(item[0], item[1], item[2]))
+
+        for item in faces:
+            thefile.write(
+                "f {0}//{0} {1}//{1} {2}//{2}\n".format(
+                    item[0], item[1], item[2]
+                )
+            )
diff --git a/demo/src/gui.py b/demo/src/gui.py
index 1d6b71a..7c6ec13 100644
--- a/demo/src/gui.py
+++ b/demo/src/gui.py
@@ -2,6 +2,7 @@
 
 import gradio as gr
 
+from .convert import nifti_to_obj
 from .css_style import css
 from .inference import run_model
 from .logger import flush_logs
@@ -9,7 +10,7 @@
 from .logger import setup_logger
 from .utils import load_ct_to_numpy
 from .utils import load_pred_volume_to_numpy
-from .utils import nifti_to_glb
+
 
 # setup logging
 LOGGER = setup_logger()
@@ -82,7 +83,7 @@ def process(self, mesh_file_name):
             name=self.result_names[self.class_name],
         )
         LOGGER.info("Converting prediction NIfTI to OBJ...")
-        nifti_to_glb("prediction.nii.gz")
+        nifti_to_obj("prediction.nii.gz")
 
         LOGGER.info("Loading CT to numpy...")
         self.images = load_ct_to_numpy(path)
@@ -113,7 +114,6 @@ def run(self):
         with gr.Blocks(css=css) as demo:
             with gr.Row():
                 with gr.Column(visible=True, scale=0.2) as sidebar_left:
-                    # gr.Markdown("SideBar Left")
                     logs = gr.Textbox(
                         placeholder="\n" * 16,
                         label="Logs",
diff --git a/demo/src/utils.py b/demo/src/utils.py
index 4dce092..4a7f9f9 100644
--- a/demo/src/utils.py
+++ b/demo/src/utils.py
@@ -1,7 +1,5 @@
 import nibabel as nib
 import numpy as np
-from nibabel.processing import resample_to_output
-from skimage.measure import marching_cubes
 
 
 def load_ct_to_numpy(data_path):
@@ -38,35 +36,3 @@ def load_pred_volume_to_numpy(data_path):
 
     print(data.shape)
     return [data[..., i] for i in range(data.shape[-1])]
-
-
-def nifti_to_glb(path, output="prediction.obj"):
-    # load NIFTI into numpy array
-    image = nib.load(path)
-    resampled = resample_to_output(image, [1, 1, 1], order=1)
-    data = resampled.get_fdata().astype("uint8")
-
-    # Create a material with a red diffuse color (RGB value)
-    red_material = "newmtl RedMaterial\nKd 1 0 0"  # Red diffuse color (RGB)
-
-    # extract surface
-    verts, faces, normals, values = marching_cubes(data, 0)
-    faces += 1
-
-    with open(output, "w") as thefile:
-        # Write the material definition to the OBJ file
-        thefile.write(red_material + "\n")
-
-        for item in verts:
-            # thefile.write('usemtl RedMaterial\n')
-            thefile.write("v {0} {1} {2}\n".format(item[0], item[1], item[2]))
-
-        for item in normals:
-            thefile.write("vn {0} {1} {2}\n".format(item[0], item[1], item[2]))
-
-        for item in faces:
-            thefile.write(
-                "f {0}//{0} {1}//{1} {2}//{2}\n".format(
-                    item[0], item[1], item[2]
-                )
-            )

From 1e90a57aeba564f1ff0ff18fe35521b33eea639c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Pedersen?= <andrped94@gmail.com>
Date: Tue, 31 Oct 2023 15:08:27 +0100
Subject: [PATCH 2/2] Minor refactoring

---
 demo/src/gui.py       | 1 -
 demo/src/inference.py | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/demo/src/gui.py b/demo/src/gui.py
index 7c6ec13..74df10d 100644
--- a/demo/src/gui.py
+++ b/demo/src/gui.py
@@ -11,7 +11,6 @@
 from .utils import load_ct_to_numpy
 from .utils import load_pred_volume_to_numpy
 
-
 # setup logging
 LOGGER = setup_logger()
 
diff --git a/demo/src/inference.py b/demo/src/inference.py
index 15a6ab1..5d3774c 100644
--- a/demo/src/inference.py
+++ b/demo/src/inference.py
@@ -91,6 +91,7 @@ def run_model(
             shutil.rmtree(patient_directory)
         if os.path.exists(output_path):
             shutil.rmtree(output_path)
+
     except Exception:
         print(traceback.format_exc())
         # Clean-up