icrdr/Bioxel
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

feat: layer list system

Browse Source
This commit is contained in:
马南
2024-08-14 14:16:40 +08:00
parent 21e0b85662
commit 9e885865f7
21 changed files with 1451 additions and 825 deletions
Download Patch File Download Diff File Expand all files Collapse all files

189
bioxelnodes/operators/io.py
View File

@@ -5,19 +5,19 @@ import threading
import numpy as np
from pathlib import Path
from ..exceptions import CancelledByUser
from ..props import BIOXELNODES_Series
from ..bioxel.layer import Layer
from ..bioxelutils.layer import (get_all_layer_objs,
get_layer_obj)
from ..bioxelutils.utils import (get_all_layer_objs, get_container_obj,
get_layer_obj,
get_container_objs_from_selection)
from ..bioxelutils.container import (Container,
add_layers,
container_to_obj,
get_container_objs_from_selection)
container_to_obj)
from ..bioxel.layer import Layer
from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS,
get_ext, parse_volumetric_data)
from .utils import (change_render_setting, get_cache_dir, get_preferences,
from .utils import (get_cache_dir,
progress_update, progress_bar, select_object)
# 3rd-party
@@ -78,20 +78,30 @@ class ImportVolumetricData():
return {'RUNNING_MODAL'}
class ImportAsScalarLayer(bpy.types.Operator, ImportVolumetricData):
bl_idname = "bioxelnodes.import_as_scalar_layer"
class ImportAsScalar(bpy.types.Operator, ImportVolumetricData):
bl_idname = "bioxelnodes.import_as_scalar"
bl_label = "Import as Scalar"
bl_description = "Import Volumetric Data to Container as Scalar"
bl_icon = "EVENT_S"
read_as = "scalar"
class ImportAsLabelLayer(bpy.types.Operator, ImportVolumetricData):
bl_idname = "bioxelnodes.import_as_label_layer"
class ImportAsLabel(bpy.types.Operator, ImportVolumetricData):
bl_idname = "bioxelnodes.import_as_label"
bl_label = "Import as Label"
bl_description = "Import Volumetric Data to Container as Label"
bl_icon = "EVENT_L"
read_as = "label"
class ImportAsColor(bpy.types.Operator, ImportVolumetricData):
bl_idname = "bioxelnodes.import_as_color"
bl_label = "Import as Label"
bl_description = "Import Volumetric Data to Container as Label"
bl_icon = "EVENT_C"
read_as = "color"
class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
bl_idname = "BIOXELNODES_FH_ImportVolumetricData"
bl_label = "File handler for dicom import"
@@ -100,7 +110,16 @@ class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
@classmethod
def poll_drop(cls, context):
return (context.area and context.area.type == 'VIEW_3D')
if not context.area:
return False
if context.area.type == 'VIEW_3D':
return True
elif context.area.type == 'NODE_EDITOR':
container_obj = get_container_obj(context.object)
return container_obj is not None
else:
return False
def get_series_ids(self, context):
@@ -125,7 +144,6 @@ class ParseVolumetricData(bpy.types.Operator):
meta = None
thread = None
_timer = None
container_obj_name = ""
progress: bpy.props.FloatProperty(name="Progress",
options={"SKIP_SAVE"},
@@ -144,7 +162,8 @@ class ParseVolumetricData(bpy.types.Operator):
read_as: bpy.props.EnumProperty(name="Read as",
default="scalar",
items=[("scalar", "Scalar", ""),
("label", "Labels", "")]) # type: ignore
("label", "Labels", ""),
("color", "Color", "")]) # type: ignore
series_id: bpy.props.EnumProperty(name="Select Series",
items=get_series_ids) # type: ignore
@@ -153,6 +172,10 @@ class ParseVolumetricData(bpy.types.Operator):
type=BIOXELNODES_Series) # type: ignore
def execute(self, context):
if not self.filepath:
self.report({"WARNING"}, "No file selected.")
return {'CANCELLED'}
data_path = Path(self.filepath).resolve()
ext = get_ext(data_path)
if ext not in SUPPORT_EXTS:
@@ -207,7 +230,7 @@ class ParseVolumetricData(bpy.types.Operator):
# Check if user press 'ESC'
if event.type == 'ESC':
self.is_cancelled = True
progress_update(context, 0, "Canceling...")
progress_update(context, 0.0, "Canceling...")
return {'PASS_THROUGH'}
# Check if is the timer time
@@ -227,6 +250,7 @@ class ParseVolumetricData(bpy.types.Operator):
context.window_manager.event_timer_remove(self._timer)
# Remove the progress bar from status bar
bpy.types.STATUSBAR_HT_header.remove(progress_bar)
progress_update(context, 1.0)
# Check if thread is cancelled by user
if self.is_cancelled:
@@ -248,23 +272,32 @@ class ParseVolumetricData(bpy.types.Operator):
orig_shape = self.meta['xyz_shape']
orig_spacing = self.meta['spacing']
if orig_spacing[2] == 1 and orig_spacing[0] < 0.1:
spacing_log10 = math.floor(math.log10(min(*orig_spacing)))
orig_spacing = (orig_spacing[0] * math.pow(10, -spacing_log10-1),
orig_spacing[1] * math.pow(10, -spacing_log10-1),
1)
min_size = min(orig_spacing[0],
orig_spacing[1], orig_spacing[2])
bioxel_size = max(min_size, 1.0)
layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
layer_size = get_layer_size(layer_shape,
bioxel_size)
log10 = math.floor(math.log10(max(*layer_size)))
log10 = max(1, log10)
log10 = min(3, log10)
scene_scale = math.pow(10, -log10)
# layer_shape = get_layer_shape(1, orig_shape, orig_spacing)
# layer_size = get_layer_size(layer_shape,
# bioxel_size)
# log10 = math.floor(math.log10(max(*layer_size)))
# log10 = max(1, log10)
# log10 = min(3, log10)
# scene_scale = math.pow(10, -log10)
scene_scale = 0.01
if self.container_obj_name:
container_obj = bpy.data.objects.get(self.container_obj_name)
if context.area.type == "NODE_EDITOR":
container_obj = context.object
container_name = container_obj.name
container_obj_name = container_name
else:
container_name = self.meta['name']
container_obj_name = ""
series_id = self.series_id if self.series_id != "empty" else ""
bpy.ops.bioxelnodes.import_volumetric_data_dialog(
@@ -278,7 +311,7 @@ class ParseVolumetricData(bpy.types.Operator):
series_id=series_id,
frame_count=self.meta['frame_count'],
channel_count=self.meta['channel_count'],
container_obj_name=self.container_obj_name,
container_obj_name=container_obj_name,
read_as=self.read_as,
scene_scale=scene_scale
)
@@ -287,18 +320,20 @@ class ParseVolumetricData(bpy.types.Operator):
return {'FINISHED'}
def invoke(self, context, event):
if not self.filepath:
if context.window_manager.bioxelnodes_progress_factor < 1:
print("A process is executing, please wait for it to finish.")
return {'CANCELLED'}
if not self.filepath:
return self.execute(context)
data_path = Path(self.filepath).resolve()
ext = get_ext(data_path)
container_objs = get_container_objs_from_selection()
if len(container_objs) > 0:
self.container_obj_name = container_objs[0].name
title = f"Add to **{self.container_obj_name}**" \
if self.container_obj_name != "" else f"Init a Container"
if context.area.type == "NODE_EDITOR":
title = f"Add to **{context.object.name}**"
else:
title = "Init a Container"
# Series Selection
if ext in DICOM_EXTS:
@@ -367,8 +402,7 @@ class ParseVolumetricData(bpy.types.Operator):
return {'CANCELLED'}
if self.skip_read_as:
self.execute(context)
return {'RUNNING_MODAL'}
return self.execute(context)
else:
context.window_manager.invoke_props_dialog(self,
width=400,
@@ -429,7 +463,8 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
read_as: bpy.props.EnumProperty(name="Read as",
default="scalar",
items=[("scalar", "Scalar", ""),
("label", "Labels", "")]) # type: ignore
("label", "Labels", ""),
("color", "Color", "")]) # type: ignore
bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)",
soft_min=0.1, soft_max=10.0,
@@ -540,12 +575,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
try:
layer = Layer(data=data == np.full_like(data, i+1),
name=name_i,
kind=kind,
affine=affine)
kind=kind)
layer.resize(shape=shape,
progress_callback=progress_callback)
layer.affine = affine
layers.append(layer)
except CancelledByUser:
return
@@ -553,6 +589,64 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
self.has_error = e
return
if kind == "color":
if np.issubdtype(np.uint8, data.dtype):
data = np.multiply(data, 1.0 / 256,
dtype=np.float32)
elif data.dtype.kind in ['u', 'i']:
min_val = data.min()
max_val = data.max()
# Avoid division by zero if all values are the same
if max_val != min_val:
# Normalize the array to the range (0,1)
data = (data - min_val) / (max_val - min_val)
else:
# If all values are the same, the normalized array will be all zeros
data = np.zeros_like(data, dtype=np.float32)
# Convert the normalized array to float dtype
data = data.astype(np.float32)
else:
data = data.astype(np.float32)
name = self.layer_name or "Color"
if data.shape[4] == 1:
data = np.repeat(data, repeats=3, axis=4)
elif data.shape[4] == 2:
d_shape = list(data.shape)
d_shape = d_shape[:4] + [1]
zore = np.zeros(tuple(d_shape), dtype=np.float32)
data = np.concatenate((data, zore), axis=-1)
elif data.shape[4] > 3:
data = data[:, :, :, :, :3]
if cancel():
return
progress_update(context, 0.2,
f"Processing {name}...")
progress_callback = progress_callback_factory(name,
0.2,
0.7)
try:
layer = Layer(data=data,
name=name,
kind=kind)
layer.resize(shape=shape,
progress_callback=progress_callback)
layer.affine = affine
layers.append(layer)
except CancelledByUser:
return
except Exception as e:
self.has_error = e
return
elif kind == "scalar":
name = self.layer_name or "Scalar"
@@ -573,12 +667,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
try:
layer = Layer(data=data[:, :, :, :, i:i+1],
name=name_i,
kind=kind,
affine=affine)
kind=kind)
layer.resize(shape=shape,
progress_callback=progress_callback)
layer.affine = affine
layers.append(layer)
except CancelledByUser:
return
@@ -598,12 +693,13 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
try:
layer = Layer(data=data,
name=name,
kind=kind,
affine=affine)
kind=kind)
layer.resize(shape=shape,
progress_callback=progress_callback)
layer.affine = affine
layers.append(layer)
except CancelledByUser:
return
@@ -634,7 +730,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
def modal(self, context, event):
if event.type == 'ESC':
self.is_cancelled = True
progress_update(context, 0, "Canceling...")
progress_update(context, 0.0, "Canceling...")
return {'PASS_THROUGH'}
if event.type != 'TIMER':
@@ -647,6 +743,7 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
self.thread.join()
context.window_manager.event_timer_remove(self._timer)
bpy.types.STATUSBAR_HT_header.remove(progress_bar)
progress_update(context, 1.0)
if self.is_cancelled:
self.report({"WARNING"}, "Canncelled by user.")
@@ -672,7 +769,8 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
container_obj=container_obj,
cache_dir=get_cache_dir(context))
else:
container = Container(name=self.container_name,
name = self.container_name or "Container"
container = Container(name=name,
layers=self.layers)
container_obj = container_to_obj(container,
@@ -683,7 +781,10 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
# Change render setting for better result
if is_first_import:
change_render_setting(context)
bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
preset="slice_viewer")
bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT',
preset="cycles_preview")
self.report({"INFO"}, "Successfully Imported")
return {'FINISHED'}