update configs and add blender parameter to snakefile

RUB-Bioinf · Feb 25, 2023 · ce3f923 · ce3f923
1 parent 3f82847
commit ce3f923
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Showing 10 changed files with 17 additions and 11 deletions.
diff --git a/VesselExpress/configs/bladder_config.json b/VesselExpress/configs/bladder_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/bone_config.json b/VesselExpress/configs/bone_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/ear_config.json b/VesselExpress/configs/ear_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 2,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/heart_config.json b/VesselExpress/configs/heart_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/liver_config.json b/VesselExpress/configs/liver_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/muscle_config.json b/VesselExpress/configs/muscle_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.5,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/spinal_cord_config.json b/VesselExpress/configs/spinal_cord_config.json
@@ -4,7 +4,6 @@
   "3D": 1,
   "render": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 3.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/configs/tongue_config.json b/VesselExpress/configs/tongue_config.json
@@ -3,8 +3,9 @@
   "segmentation": "segmentation3D",
   "3D": 1,
   "render": 0,
+  "marching_cubes": 0,
+  "small_RAM_mode": 0,
   "segmentation3D": {
-    "small_RAM_mode": 0,
     "smoothing": 1,
     "core_threshold": 4.0,
     "core_vessel_1": 1,

diff --git a/VesselExpress/workflow/Snakefile b/VesselExpress/workflow/Snakefile
@@ -181,7 +181,7 @@ rule renderBinary:
     shell:
             BLENDER_PATH + " --background --python " + SCRIPT_PATH + "/render_object.py -- -model_file_path \"{input}\" -out_dir \"{PATH}/{wildcards.img}/\" \
             -save_raw {config[rendering][save_raw]} -save_glb {config[rendering][save_glb]} -render_device {config[rendering][render_device]} \
-            -render_distance {config[rendering][render_distance]} \
+            -background_transparent {config[rendering][background_transparent]} -render_distance {config[rendering][render_distance]} \
             -image_resolution_x {config[rendering][image_resolution_x]} \
             -image_resolution_y {config[rendering][image_resolution_y]} \
             -image_compression {config[rendering][image_compression]} \
@@ -206,7 +206,7 @@ rule renderSkeleton:
     shell:
             BLENDER_PATH + " --background --python " + SCRIPT_PATH + "/render_object.py -- -model_file_path \"{input}\" -out_dir \"{PATH}/{wildcards.img}/\" \
             -save_raw {config[rendering][save_raw]} -save_glb {config[rendering][save_glb]} -render_device {config[rendering][render_device]} \
-            -render_distance {config[rendering][render_distance]} \
+            -background_transparent {config[rendering][background_transparent]} -render_distance {config[rendering][render_distance]} \
             -image_resolution_x {config[rendering][image_resolution_x]} \
             -image_resolution_y {config[rendering][image_resolution_y]} \
             -image_compression {config[rendering][image_compression]} \

diff --git a/VesselExpress/workflow/envs/Linux/Pipeline.yml b/VesselExpress/workflow/envs/Linux/Pipeline.yml
@@ -1,4 +1,4 @@
-name: Segmentation
+name: Pipeline
 channels:
   - defaults
 dependencies: