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Merge pull request #36 from OmooLab/feature/dev

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Feature/dev
This commit is contained in:
Ma Nan
2024-08-05 15:54:19 +08:00
committed by GitHub
parent 088d9c1edb 2563f398da
commit 2429eef5e0
5 changed files with 78 additions and 70 deletions
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29
bioxelnodes/bioxel/parse.py
View File

@@ -14,22 +14,23 @@ Convert any volumetric data to 3D numpy array with order TXYZC
"""
SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
'.ome.tiff', '.ome.tif',
'.tif', '.TIF', '.tiff', '.TIFF',
'.mrc', '.mrc.gz', '.map', '.map.gz',
'.bmp', '.BMP',
'.png', '.PNG',
'.jpg', '.JPG', '.jpeg', '.JPEG',
'.PIC', '.pic',
'.gipl', '.gipl.gz',
'.jpg', '.JPG', '.jpeg', '.JPEG',
'.lsm', '.LSM',
'.tif', '.TIF', '.tiff', '.TIFF',
'.mnc', '.MNC',
'.mrc', '.rec',
'.mha', '.mhd',
'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
'.nrrd', '.nhdr',
'.png', '.PNG',
'.vtk',
'.ome.tiff', '.ome.tif',
'.mrc', '.mrc.gz', '.map', '.map.gz']
'.gz']
OME_EXTS = ['.ome.tiff', '.ome.tif',
'.tif', '.TIF', '.tiff', '.TIFF']
@@ -68,7 +69,7 @@ def get_file_name(filepath: Path):
return filepath.name.removesuffix(ext).replace(" ", "-")
def get_file_index(filepath: Path):
def get_file_number(filepath: Path) -> str:
name = get_file_name(filepath)
digits = ""
@@ -85,15 +86,18 @@ def get_file_index(filepath: Path):
break
# Reverse the digits string to get the correct order
last_number = digits[::-1]
return int(last_number) if last_number != "" else 0
return digits[::-1]
def get_sequence_name(filepath: Path) -> str:
name = get_file_name(filepath)
index = get_file_index(filepath)
return name.removesuffix(str(index))
number = get_file_number(filepath)
return name.removesuffix(number)
def get_sequence_index(filepath: Path) -> int:
number = get_file_number(filepath)
return int(number) if number != "" else 0
def collect_sequence(filepath: Path):
@@ -102,9 +106,10 @@ def collect_sequence(filepath: Path):
if f.is_file() \
and get_ext(filepath) == get_ext(f) \
and get_sequence_name(filepath) == get_sequence_name(f):
index = get_file_index(f)
index = get_sequence_index(f)
file_dict[index] = f
# reomve isolated seq file
for key in file_dict.copy().keys():
if not file_dict.get(key+1) \
and not file_dict.get(key-1):

2
bioxelnodes/blender_manifest.toml
View File

@@ -1,7 +1,7 @@
schema_version = "1.0.0"
id = "bioxelnodes"
version = "0.3.1"
version = "0.3.2"
name = "Bioxel Nodes"
tagline = "For scientific volumetric data visualization in Blender"
maintainer = "Ma Nan <icrdr2010@outlook.com>"

103
bioxelnodes/operators/io.py
View File

@@ -24,19 +24,6 @@ from .utils import (change_render_setting, get_cache_dir, get_preferences,
import SimpleITK as sitk
import transforms3d
FH_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
'.gipl', '.gipl.gz',
'.mnc', '.MNC',
'.mrc', '.rec',
'.mha', '.mhd',
'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
'.nrrd', '.nhdr',
'.vtk',
'.gz'
'.ome.tiff', '.ome.tif',
'.mrc', '.mrc.gz', '.map', '.map.gz']
def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
@@ -69,24 +56,20 @@ class ImportVolumetricData():
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
read_as = "scalar"
def execute(self, context):
container_objs = get_container_objs_from_selection()
data_path = Path(self.filepath).resolve()
ext = get_ext(data_path)
if ext not in SUPPORT_EXTS:
self.report({"WARNING"}, "Not supported format.")
return {'CANCELLED'}
if len(container_objs) > 0:
bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT',
filepath=self.filepath,
directory=self.directory,
container_obj_name=container_objs[0].name,
read_as=self.read_as)
else:
bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT',
filepath=self.filepath,
directory=self.directory,
read_as=self.read_as)
bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT',
filepath=self.filepath,
skip_read_as=True,
read_as=self.read_as)
return {'FINISHED'}
@@ -113,7 +96,7 @@ class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler):
bl_idname = "BIOXELNODES_FH_ImportVolumetricData"
bl_label = "File handler for dicom import"
bl_import_operator = "bioxelnodes.parse_volumetric_data"
bl_file_extensions = ";".join(FH_EXTS)
bl_file_extensions = ";".join(SUPPORT_EXTS)
@classmethod
def poll_drop(cls, context):
@@ -135,21 +118,26 @@ def get_series_ids(self, context):
class ParseVolumetricData(bpy.types.Operator):
bl_idname = "bioxelnodes.parse_volumetric_data"
bl_label = "Import Volumetric Data"
bl_label = "Import Volumetric Data (BioxelNodes)"
bl_description = "Import Volumetric Data as Layer"
bl_options = {'UNDO'}
meta = None
thread = None
_timer = None
container_obj_name = ""
progress: bpy.props.FloatProperty(name="Progress",
options={"SKIP_SAVE"},
default=1) # type: ignore
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
container_obj_name: bpy.props.StringProperty() # type: ignore
skip_read_as: bpy.props.BoolProperty(name="Skip Read As",
default=False) # type: ignore
skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select",
default=True) # type: ignore
read_as: bpy.props.EnumProperty(name="Read as",
default="scalar",
@@ -166,7 +154,7 @@ class ParseVolumetricData(bpy.types.Operator):
data_path = Path(self.filepath).resolve()
ext = get_ext(data_path)
if ext not in SUPPORT_EXTS:
self.report({"WARNING"}, "Not supported extension.")
self.report({"WARNING"}, "Not supported format.")
return {'CANCELLED'}
print("Collecting Meta Data...")
@@ -297,12 +285,19 @@ class ParseVolumetricData(bpy.types.Operator):
return {'FINISHED'}
def invoke(self, context, event):
if not self.filepath and not self.directory:
if not self.filepath:
return {'CANCELLED'}
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"
# Series Selection
if ext in DICOM_EXTS:
data_dirpath = data_path.parent
@@ -358,9 +353,10 @@ class ParseVolumetricData(bpy.types.Operator):
series_item.label = value
if len(series_items.keys()) > 1:
self.skip_series_select = False
context.window_manager.invoke_props_dialog(self,
width=400,
title="Which series to import?")
title=title)
return {'RUNNING_MODAL'}
elif len(series_items.keys()) == 1:
self.series_id = list(series_items.keys())[0]
@@ -368,27 +364,37 @@ class ParseVolumetricData(bpy.types.Operator):
self.report({"ERROR"}, "Get no vaild series.")
return {'CANCELLED'}
self.execute(context)
return {'RUNNING_MODAL'}
if self.skip_read_as:
self.execute(context)
return {'RUNNING_MODAL'}
else:
context.window_manager.invoke_props_dialog(self,
width=400,
title=title)
return {'RUNNING_MODAL'}
def draw(self, context):
layout = self.layout
layout.label(
text='Detect multi-series in DICOM, pick one')
layout.prop(self, "series_id")
if not self.skip_read_as:
layout.label(
text='What kind is the data read as?')
layout.prop(self, "read_as")
if not self.skip_series_select:
layout.label(text='Which series to import?')
layout.prop(self, "series_id")
def get_sequence_sources(self, context):
items = [("-1", "None (Static)", "")]
items = [("-1", "None (1 frame)", "")]
orig_shape = tuple(self.orig_shape)
if self.frame_count > 1:
items.append(("0", f"Frame (Get {self.frame_count} frames)", ""))
items.append(("0", f"Frame ({self.frame_count} frames)", ""))
elif self.frame_count == 1 and self.channel_count > 1:
items.append(("4", f"Channel (Get {self.channel_count} frames)", ""))
items.append(("4", f"Channel ({self.channel_count} frames)", ""))
elif self.frame_count == 1 and self.channel_count == 1:
items.append(("1", f"X (Get {orig_shape[0]} frames)", ""))
items.append(("2", f"Y (Get {orig_shape[1]} frames)", ""))
items.append(("3", f"Z (Get {orig_shape[2]} frames)", ""))
items.append(("1", f"X ({orig_shape[0]} frames)", ""))
items.append(("2", f"Y ({orig_shape[1]} frames)", ""))
items.append(("3", f"Z ({orig_shape[2]} frames)", ""))
return items
@@ -681,12 +687,9 @@ class ImportVolumetricDataDialog(bpy.types.Operator):
return {'FINISHED'}
def invoke(self, context, event):
if self.read_as == "label":
volume_dtype = "Label"
elif self.read_as == "scalar":
volume_dtype = "Scalar"
title = f"As {volume_dtype} Opitons (Add to Container: {self.container_obj_name})" \
if self.container_obj_name != "" else f"As {volume_dtype} Options (Init a Container)"
layer_kind = self.read_as.capitalize()
title = f"Add to **{self.container_obj_name}**, As {layer_kind}" \
if self.container_obj_name != "" else f"Init a Container, As {layer_kind}"
context.window_manager.invoke_props_dialog(self,
width=500,
title=title)

12
bioxelnodes/operators/misc.py
View File

@@ -61,8 +61,8 @@ class SaveStagedData(bpy.types.Operator):
bl_label = "Save Staged Data"
bl_description = "Save all staged data in this file for sharing"
save_layer: bpy.props.BoolProperty(
name="Save Layer VDB Cache",
save_cache: bpy.props.BoolProperty(
name="Save Layer Caches",
default=True,
) # type: ignore
@@ -112,11 +112,11 @@ class SaveStagedData(bpy.types.Operator):
self.report({"INFO"}, f"Successfully saved to {output_path}")
if self.save_layer:
if self.save_cache:
fails = []
for layer in get_all_layer_objs():
try:
save_layer(layer, self.cache_dir)
save_layer_cache(layer, self.cache_dir)
except:
fails.append(layer)
@@ -140,7 +140,7 @@ class SaveStagedData(bpy.types.Operator):
def draw(self, context):
layout = self.layout
panel = layout.box()
panel.prop(self, "save_layer")
panel.prop(self, "save_cache")
panel.prop(self, "cache_dir")
panel = layout.box()
panel.prop(self, "save_lib")
@@ -148,7 +148,7 @@ class SaveStagedData(bpy.types.Operator):
class SaveCaches(bpy.types.Operator):
bl_idname = "bioxelnodes.save_layers"
bl_idname = "bioxelnodes.save_caches"
bl_label = "Save Caches"
bl_description = "Save Container's caches to directory."

2
pyproject.toml
View File

@@ -1,6 +1,6 @@
[tool.poetry]
name = "bioxelnodes"
version = "0.3.1"
version = "0.3.2"
description = ""
authors = ["Ma Nan <icrdr2010@outlook.com>"]
license = "MIT"