tomcat blender up to date

03_nc_to_npy_for_openvdb.py

@@ -62,7 +62,7 @@ class volume_maker:
     def clean_binary_image(self, im, clean = True, remove_small=True,  minsize = 20, fp_radius = 1, i=0, GPU = True, GPU_avail=GPU_avail):
         if clean or remove_small:
             if GPU and GPU_avail:
-                gpu_id = i%4+1 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
+                gpu_id = i%5 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
         
                 with cp.cuda.Device(gpu_id):
                     im = cp.array(im)
@@ -87,7 +87,7 @@ class volume_maker:
             mask = self.data[self.mask_name].sel(timestep = ts).data
             
             if GPU and GPU_avail:
-                gpu_id = i%4+1 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
+                gpu_id = i%5 #num_GPU #use gpus 1 through 4, leaving the big A40 (0) alone or i%5 to use all 5
         
                 with cp.cuda.Device(gpu_id):
                     mask = cp.array(mask)

04_CL_npy_to_openvdb_in_blender.py

@@ -0,0 +1,46 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Jun 20 14:53:48 2023
+
+converts numpy array to openvdb
+
+run within blender to use pyopenvdb, it would eventually be nice to use pyopenvdb outside blender to have the conversion in one go
+
+@author: fische_r
+"""
+
+import os
+import numpy as np
+import pyopenvdb as openvdb
+
+
+sample = '3II'
+ts = 28
+
+inpath = os.path.join('/mpc/homes/fische_r/NAS/DASCOELY/processing/06_anode_CL', sample, str(ts)+'_cropped_to_membrane_ML.npy')
+outpath = os.path.join('/mpc/homes/fische_r/NAS/DASCOELY/processing/06_anode_CL', sample, str(ts)+'_cropped_to_membrane_ML.vdb')
+#modified crops, comment out
+x1 = 20
+x2 = -20
+y1 = 0
+y2 = -1
+z1 = 20
+z2 = -20
+
+def convert_npy_to_vdb(inpath, outpath, x1, x2, y1,y2, z1, z2):
+    im = np.load(inpath)
+    im = im[x1:x2,y1:y2,z1:z2]
+
+    
+    grid = openvdb.FloatGrid()
+    grid.copyFromArray(im.astype(float))
+    grid.gridClass = openvdb.GridClass.FOG_VOLUME
+    grid.name = 'density'
+    
+    openvdb.write(outpath, grid)
+    
+
+
+convert_npy_to_vdb(inpath, outpath, x1, x2, y1,y2, z1, z2)
+
+

04_npy_to_openvdb_in_blender.py

@@ -14,8 +14,8 @@ import numpy as np
 import pyopenvdb as openvdb
 
 
-toppath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5II/all_phases_npy'
-topoutpath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/5II/combined_vdb'
+toppath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/4/all_phases_npy'
+topoutpath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/04_membrane_ML/4/combined_vdb'
 
 if not os.path.exists(topoutpath):
     os.mkdir(topoutpath)

npy_to_vdb.py

@@ -0,0 +1,21 @@
+import bpy
+import pyopenvdb as openvdb
+import numpy as np
+
+Volume = np.load('/mpc/homes/fische_r/NAS/DASCOELY/processing/02_registered_3p1D/3II_ts_4_registered.npy')
+Volume = Volume/25000
+Volume = Volume[20:-20,20:-20,200:-500]
+
+grid = openvdb.FloatGrid()
+
+grid.copyFromArray(Volume.astype(float))
+
+
+#grid.transform = openvdb.createLinearTransform([[1, 0, 0, 0,], [0, 1, 0, 0], [0,0,1,0],[0,0,0,1]])
+
+grid.gridClass = openvdb.GridClass.FOG_VOLUME
+grid.name = 'density'
+
+openvdb.write('/mpc/homes/fische_r/NAS/DASCOELY/processing/02_registered_3p1D/3II_ts_4_registered.vdb', grid)
+
+bpy.ops.object.volume_import(filepath = '/mpc/homes/fische_r/NAS/DASCOELY/processing/02_registered_3p1D/3II_ts_4_registered.vdb', files=[])