Merge pull request #49 from oanegros/development

Hotfixes volume size and test if material autogen things are there, restricts numpy to v1

Makefile

@@ -6,6 +6,8 @@ test:
 version := $(shell grep version pyproject.toml | grep -o -E "\b[0-9]+\.[0-9]+\.[0-9]+\b")
 
 template:
+	mkdir tif2blender/assets
+	mkdir tif2blender/assets/template
 	cd tif2blender/assets/template && zip -r tif2blender.zip ../../../tif2blender
 
 # git clean -dfX

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tif2blender"
-version = "1.0.0"
+version = "1.0.1"
 description = "Loading and handling microscopy data in Blender."
 authors = ["Oane Gros <oane.gros@embl.de>"]
 include = [
@@ -12,6 +12,7 @@ python = "~=3.11.6"
 bpy = ">=4.1.0"
 tifffile = "==2023.4.12"
 scikit-image = "==0.22.0"
+numpy = "< 2.0.0"
 
 
 [tool.poetry.dev-dependencies]

tif2blender/load_components/load_axes.py

@@ -161,6 +161,9 @@ def init_material_axes():
     links.new(trbsdf.outputs[0], mix.inputs[2])
     links.new(and_op.outputs[0], mix.inputs[0])
 
+    if nodes.get("Material Output") is None:
+            outnode = nodes.new(type='ShaderNodeOutputMaterial')
+            outnode.name = 'Material Output'
     out = nodes.get("Material Output")
     out.location = (650, 0)
     links.new(mix.outputs[0], out.inputs[0])

tif2blender/load_components/load_labelmask.py

@@ -22,6 +22,9 @@ def labelmask_shader(maskchannel, maxval):
         except Exception as e:
             print(e)
         princ = nodes.new("ShaderNodeBsdfPrincipled")
+        if nodes.get("Material Output") is None:
+            outnode = nodes.new(type='ShaderNodeOutputMaterial')
+            outnode.name = 'Material Output'
         links.new(princ.outputs[0], nodes.get('Material Output').inputs[0])
 
     idnode =  nodes.new("ShaderNodeVertexColor")
@@ -181,6 +184,7 @@ def export_alembic_and_loc(mask, maskchannel, cache_dir, remake, axes_order):
 
         if Path(fname).exists() and remake:
             Path(fname).unlink() # this may fix an issue with subsequent loads
+
         bpy.ops.wm.alembic_export(filepath=fname,
                         visible_objects_only=False,
                         selected=True,
@@ -211,7 +215,7 @@ def import_abc_and_loc(maskchannel, scale, cache_dir):
 
     channel_collection, _ = make_subcollection(f"channel {maskchannel} labelmask")
     bpy.ops.wm.alembic_import(filepath=abcfname(cache_dir, maskchannel, 0), is_sequence=True)
-
+    
     with open(jsonfname(cache_dir, maskchannel), 'r') as fp:
         locations = json.load(fp)
 

tif2blender/load_components/load_volume.py

@@ -16,7 +16,7 @@ def arrays_to_vdb_files(volume_arrays, axes_order, remake, cache_dir):
     for ch in volume_arrays:
         volume_arrays[ch]['vdbs'] = []
         imgdata = volume_arrays[ch]['data']
-        n_splits = [(imgdata.shape[dim] // 50)+ 1 for dim in [axes_order.find('x'),axes_order.find('y'),axes_order.find('z')]]
+        n_splits = [(imgdata.shape[dim] // 2049)+ 1 for dim in [axes_order.find('x'),axes_order.find('y'),axes_order.find('z')]]
         a_chunks = np.array_split(imgdata, n_splits[0], axis=axes_order.find('x'))
         for a_ix, a_chunk in enumerate(a_chunks):
             b_chunks = np.array_split(a_chunk, n_splits[1], axis=axes_order.find('y'))
@@ -102,7 +102,10 @@ def volume_materials(volume_inputs, emission_setting):
         add.location = (450, -300)
         links.new(adsorb.outputs[0], add.inputs[0])
         links.new(scatter.outputs[0], add.inputs[1])
-
+
+        if nodes.get("Material Output") is None:
+            outnode = nodes.new(type='ShaderNodeOutputMaterial')
+            outnode.name = 'Material Output'
         nodes.get("Material Output").location = (700,00)
         if emission_setting:
             links.new(emit.outputs[0], nodes.get("Material Output").inputs.get('Volume'))
@@ -145,6 +148,8 @@ def load_volume(volume_inputs, bbox_px, scale, cache_coll, base_coll, emission_s
     for mat in vol_obj.data.materials:
         # make sure color ramp is immediately visibile under Volume shader
         # mat.node_tree.nodes["Slice Cube"].inputs[0].show_expanded = True
-        mat.node_tree.nodes["Emission"].inputs[0].show_expanded = True
-
+        try:
+            mat.node_tree.nodes["Emission"].inputs[0].show_expanded = True
+        except:
+            pass
     return vol_obj, volume_inputs