some mods to blender scripts, formatted TODO in README

README.md

@@ -3,10 +3,12 @@
 ![lstopo](img/tomcat_blender_logo_sketch.png)
 
 Scripts to automate TOMCAT data visualization in blender with python.
-TODO: make cool logo from current sketch
-TODO: build into python module with classes
-TODO: maybe wrap system call of blender
-TODO: add cupy/cucim support
+TODO:
+- [ ] make cool logo from current sketch
+- [ ] build into python module with classes
+- [ ] maybe wrap system call of blender
+- [x] add cupy/cucim support (partly done)
+- [ ] use openvdb for volume import in blender
 
 required packages: xarray, scikit-image, trimesh, numpy
 
@@ -23,4 +25,4 @@ required packages: xarray, scikit-image, trimesh, numpy
 	```bash
 	<path_to_binary>blender.exe blend-file.blend --background --python testanimscriptfull.py
 	```
-1. (optional) adjust frame and sampling rate, better option: create separate avi-files, merge and convert to mkv, e.g. combining ImageJ and ffmpeg
+1. (optional) adjust frame and sampling rate, better option: create separate avi-files, merge and convert to mkv, e.g. combining ImageJ and ffmpeg

animscript_full.py

@@ -2,10 +2,11 @@ import bpy
 import os
 
 baseFolder="/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/membrane_smaller_200_removed/" #for stl
-outfolder="/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/membrane_cathode_camera_png/" #for png
+baseFolder2 = "/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/crack_smaller_200_removed/" 
+outfolder="/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/membrane_crack_anode_camera_png/" #for png
 
 material = 'membrane' #'Crack'
-
+material2 =  'Crack'
 
 if not os.path.exists(outfolder):
     os.mkdir(outfolder)
@@ -20,12 +21,17 @@ bpy.ops.object.delete(confirm=False)
 
 
 mat = bpy.data.materials[material]
+mat2 = bpy.data.materials[material2]
 
-def load_and_render_stl(filename, baseFolder=baseFolder, mat=mat, outfolder=outfolder):
+def load_and_render_stl(filename, filename2, baseFolder=baseFolder, mat=mat, outfolder=outfolder):
 	name = filename[:-4]
-	
+	name2 = filename2[:-4]
+
 	bpy.ops.import_mesh.stl(filepath=os.path.join(baseFolder, filename), axis_up='-Z')
 	bpy.data.objects[name].data.materials.append(mat)
+
+	bpy.ops.import_mesh.stl(filepath=os.path.join(baseFolder2, filename2), axis_up='-Z')
+	bpy.data.objects[name2].data.materials.append(mat2)
 	
 	outfile = os.path.join(outfolder, ''.join([name,'.png']))
 	bpy.context.scene.render.filepath = outfile
@@ -37,8 +43,9 @@ def load_and_render_stl(filename, baseFolder=baseFolder, mat=mat, outfolder=outf
 	bpy.ops.object.delete(confirm=False)
 	
 filenames = os.listdir(baseFolder)
+filenames2 = os.listdir(baseFolder2)
 
-for filename in filenames:
+for (filename, filename2) in zip(filenames,filenames2):
 	if filename[-3:]=='stl':
-		load_and_render_stl(filename)
+		load_and_render_stl(filename, filename2)
 	

animscript_full_crack.py

@@ -0,0 +1,44 @@
+import bpy
+import os
+
+baseFolder="/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/crack_smaller_200_removed/" #for stl
+outfolder="/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/3II/crack_anode_camera_png/" #for png
+
+material = 'Crack' #'Crack'
+
+
+if not os.path.exists(outfolder):
+    os.mkdir(outfolder)
+
+# print('Warning: this is a crude hack. Make sure the names are capturing the correct objects')
+
+#delete old reference object
+name = 'reference'
+bpy.ops.object.select_all(action='DESELECT')
+bpy.data.objects[name].select_set(True)
+bpy.ops.object.delete(confirm=False)
+
+
+mat = bpy.data.materials[material]
+
+def load_and_render_stl(filename, baseFolder=baseFolder, mat=mat, outfolder=outfolder):
+	name = filename[:-4]
+	
+	bpy.ops.import_mesh.stl(filepath=os.path.join(baseFolder, filename), axis_up='-Z')
+	bpy.data.objects[name].data.materials.append(mat)
+	
+	outfile = os.path.join(outfolder, ''.join([name,'.png']))
+	bpy.context.scene.render.filepath = outfile
+	bpy.ops.render.render(write_still=True)
+	
+	#clean up
+	bpy.ops.object.select_all(action='DESELECT')
+	bpy.data.objects[name].select_set(True)
+	bpy.ops.object.delete(confirm=False)
+	
+filenames = os.listdir(baseFolder)
+
+for filename in filenames:
+	if filename[-3:]=='stl':
+		load_and_render_stl(filename)
+