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feat: support more format

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feat: support .mrc .map
feat: support .ome.tif
feat: improved user experience for importing
feat: better contrast algorithm
This commit is contained in:
马南
2024-07-22 08:51:12 +08:00
parent b2791e3aae
commit 854af4c3bc
15 changed files with 1407 additions and 704 deletions
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4
bioxelnodes/__init__.py
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@@ -9,7 +9,7 @@ bl_info = {
"author": "Ma Nan",
"description": "",
"blender": (4, 1, 0),
"version": (0, 2, 7),
"version": (0, 2, 8),
"location": "File -> Import",
"warning": "",
"category": "Node"
@@ -20,6 +20,8 @@ auto_load.init()
def register():
auto_load.register()
bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty()
bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty()
menus.add()

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bioxelnodes/assets/Nodes/BioxelNodes_4.1.blend LFS
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4
bioxelnodes/exceptions.py Normal file
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@@ -0,0 +1,4 @@
class CancelledByUser(Exception):
def __init__(self):
message = 'Cancelled by user'
super().__init__(message)

1420
bioxelnodes/io.py
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File diff suppressed because it is too large Load Diff

10
bioxelnodes/menus.py
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@@ -3,7 +3,7 @@ import bpy
from .utils import get_container_from_selection
from .operators import (AddPieCutter, AddPlaneCutter, AddCylinderCutter, AddCubeCutter, AddSphereCutter, CombineLabels,
ConvertToMesh, InvertScalar, FillByLabel, FillByThreshold, FillByRange, PickBboxWire, PickMesh, PickVolume)
from .io import ExportVolumeData, ImportAsLabelLayer, ImportAsScalarLayer
from .io import ExportVolumetricData, ImportAsLabelLayer, ImportAsScalarLayer
from .save import CleanAllCaches, ReLinkNodes, SaveLayers, SaveStagedData
@@ -115,7 +115,7 @@ class BioxelNodesOutlinerMenu(bpy.types.Menu):
layout.operator(FillByLabel.bl_idname)
layout.operator(CombineLabels.bl_idname)
layout.separator()
layout.operator(ExportVolumeData.bl_idname)
layout.operator(ExportVolumetricData.bl_idname)
def TOPBAR_FILE_IMPORT(self, context):
@@ -131,7 +131,7 @@ def TOPBAR_FILE_IMPORT(self, context):
def TOPBAR_FILE_EXPORT(self, context):
layout = self.layout
layout.separator()
layout.operator(ExportVolumeData.bl_idname,
layout.operator(ExportVolumetricData.bl_idname,
text="Bioxel Layer (.vdb)")
@@ -171,8 +171,8 @@ class BioxelNodesTopbarMenu(bpy.types.Menu):
def TOPBAR(self, context):
layout = self.layout
layout.menu(BioxelNodesTopbarMenu.bl_idname)
def add():
bpy.types.TOPBAR_MT_file_import.append(TOPBAR_FILE_IMPORT)
bpy.types.TOPBAR_MT_file_export.append(TOPBAR_FILE_EXPORT)

6
bioxelnodes/operators.py
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@@ -366,7 +366,7 @@ class FillByThreshold(bpy.types.Operator):
def invoke(self, context, event):
base_layer = get_layer(bpy.context.active_object)
scalar_min = get_layer_meta(base_layer, "Scalar Min")
self.fill_value = scalar_min
self.fill_value = min(scalar_min,0)
context.window_manager.invoke_props_dialog(self, width=400)
return {'RUNNING_MODAL'}
@@ -449,7 +449,7 @@ class FillByRange(bpy.types.Operator):
def invoke(self, context, event):
base_layer = get_layer(bpy.context.active_object)
scalar_min = get_layer_meta(base_layer, "Scalar Min")
self.fill_value = scalar_min
self.fill_value = min(scalar_min,0)
context.window_manager.invoke_props_dialog(self, width=400)
return {'RUNNING_MODAL'}
@@ -533,7 +533,7 @@ class FillByLabel(bpy.types.Operator):
def invoke(self, context, event):
base_layer = get_layer(bpy.context.active_object)
scalar_min = get_layer_meta(base_layer, "Scalar Min")
self.fill_value = scalar_min
self.fill_value = min(scalar_min,0)
context.window_manager.invoke_props_dialog(self, width=400)
return {'RUNNING_MODAL'}

369
bioxelnodes/parse.py Normal file
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@@ -0,0 +1,369 @@
from pathlib import Path
import numpy as np
from .exceptions import CancelledByUser
from .utils import get_text_index_str
try:
import SimpleITK as sitk
from pyometiff import OMETIFFReader
import mrcfile
except:
...
SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
'.bmp', '.BMP',
'.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']
OME_EXTS = ['.ome.tiff', '.ome.tif',
'.tif', '.TIF', '.tiff', '.TIFF']
MRC_EXTS = ['.mrc', '.mrc.gz', '.map', '.map.gz']
SEQUENCE_EXTS = ['.bmp', '.BMP',
'.jpg', '.JPG', '.jpeg', '.JPEG',
'.tif', '.TIF', '.tiff', '.TIFF',
'.png', '.PNG']
DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
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']
def get_ext(filepath: str) -> str:
file_path = Path(filepath)
if file_path.name.endswith(".nii.gz"):
return ".nii.gz"
elif file_path.name.endswith(".img.gz"):
return ".img.gz"
elif file_path.name.endswith(".gipl.gz"):
return ".gipl.gz"
elif file_path.name.endswith(".ome.tiff"):
return ".ome.tiff"
elif file_path.name.endswith(".ome.tif"):
return ".ome.tif"
elif file_path.name.endswith(".mrc.gz"):
return ".mrc.gz"
elif file_path.name.endswith(".map.gz"):
return ".map.gz"
else:
return file_path.suffix
def get_sequence_name(filepath: str) -> str:
ext = get_ext(filepath)
filename = Path(filepath).name.removesuffix(ext)
index: str = get_text_index_str(filename)
return filename.removesuffix(index)
def get_sequence_index(filepath: str) -> int:
ext = get_ext(filepath)
filename = Path(filepath).name.removesuffix(ext)
index: str = get_text_index_str(filename)
return int(index) if index else 0
def collect_sequence(filepath: str):
file_path = Path(filepath).resolve()
files = list(file_path.parent.iterdir())
file_dict = {}
for file in files:
if file.is_file() \
and get_ext(file_path) == get_ext(file) \
and get_sequence_name(file_path) == get_sequence_name(file):
file_dict[get_sequence_index(file)] = file
for key in file_dict.copy().keys():
if not file_dict.get(key+1) \
and not file_dict.get(key-1):
del file_dict[key]
file_dict = dict(sorted(file_dict.items()))
sequence = [str(f) for f in file_dict.values()]
if len(sequence) == 0:
sequence = [str(file_path)]
return sequence
def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
"""Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
Args:
filepath (str): file path
series_id (str, optional): DICOM series id. Defaults to "".
Returns:
_type_: _description_
"""
ext = get_ext(filepath)
if progress_callback:
progressing = progress_callback(0, "Reading the Data...")
if not progressing:
raise CancelledByUser
is_sequence = False
if ext in SEQUENCE_EXTS:
sequence = collect_sequence(filepath)
if len(sequence) > 1:
is_sequence = True
if ext in MRC_EXTS and not is_sequence:
# TODO: much to do with mrc
with mrcfile.open(filepath) as mrc:
volume = mrc.data
# mrc.print_header()
# print(volume.shape)
# print(mrc.voxel_size)
if mrc.is_single_image():
volume = np.expand_dims(volume, axis=0) # expend frame
volume = np.expand_dims(volume, axis=-1) # expend Z
volume = np.expand_dims(volume, axis=-1) # expend channel
elif mrc.is_image_stack():
volume = np.expand_dims(volume, axis=-1) # expend Z
volume = np.expand_dims(volume, axis=-1) # expend channel
elif mrc.is_volume():
volume = np.expand_dims(volume, axis=0) # expend frame
volume = np.expand_dims(volume, axis=-1) # expend channel
elif mrc.is_volume_stack():
volume = np.expand_dims(volume, axis=-1) # expend channel
name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
shape = volume.shape[1:4]
spacing = (mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z)
meta = {
"name": name,
"description": "",
"shape": shape,
"spacing": spacing,
"origin": (0, 0, 0),
"direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
"frame_count": volume.shape[0],
"channel_count": volume.shape[-1],
"is_oriented": False
}
elif ext in OME_EXTS and not is_sequence:
reader = OMETIFFReader(fpath=filepath)
ome_volume, metadata, xml_metadata = reader.read()
if progress_callback:
progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
if not progressing:
raise CancelledByUser
try:
# print(ome_volume.shape)
# for key in metadata:
# print(f"{key},{metadata[key]}")
ome_order = metadata['DimOrder BF Array']
except:
ome_order = "TCZYX"
if ome_volume.ndim == 2:
ome_order = ome_order.replace("T", "")\
.replace("C", "").replace("Z", "")
bioxel_order = (ome_order.index('X'),
ome_order.index('Y'))
volume = np.transpose(ome_volume, bioxel_order)
volume = np.expand_dims(volume, axis=0) # expend frame
volume = np.expand_dims(volume, axis=-1) # expend Z
volume = np.expand_dims(volume, axis=-1) # expend channel
elif ome_volume.ndim == 3:
# -> XYZC
ome_order = ome_order.replace("T", "").replace("C", "")
bioxel_order = (ome_order.index('X'),
ome_order.index('Y'),
ome_order.index('Z'))
volume = np.transpose(ome_volume, bioxel_order)
volume = np.expand_dims(volume, axis=0) # expend frame
volume = np.expand_dims(volume, axis=-1) # expend channel
elif ome_volume.ndim == 4:
# -> XYZC
ome_order = ome_order.replace("T", "")
bioxel_order = (ome_order.index('X'),
ome_order.index('Y'),
ome_order.index('Z'),
ome_order.index('C'))
volume = np.transpose(ome_volume, bioxel_order)
volume = np.expand_dims(volume, axis=0) # expend frame
elif ome_volume.ndim == 5:
# -> TXYZC
bioxel_order = (ome_order.index('T'),
ome_order.index('X'),
ome_order.index('Y'),
ome_order.index('Z'),
ome_order.index('C'))
volume = np.transpose(ome_volume, bioxel_order)
shape = volume.shape[1:4]
try:
spacing = (metadata['PhysicalSizeX'],
metadata['PhysicalSizeY'],
metadata['PhysicalSizeZ'])
except:
spacing = (1, 1, 1)
name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
meta = {
"name": name,
"description": "",
"shape": shape,
"spacing": spacing,
"origin": (0, 0, 0),
"direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
"frame_count": volume.shape[0],
"channel_count": volume.shape[-1],
"is_oriented": False
}
else:
if ext in DICOM_EXTS:
dir_path = Path(filepath).resolve().parent
reader = sitk.ImageSeriesReader()
reader.MetaDataDictionaryArrayUpdateOn()
reader.LoadPrivateTagsOn()
series_files = reader.GetGDCMSeriesFileNames(
str(dir_path), series_id)
reader.SetFileNames(series_files)
itk_volume = reader.Execute()
# for k in reader.GetMetaDataKeys(0):
# v = reader.GetMetaData(0, k)
# print(f'({k}) = = "{v}"')
def get_meta(key):
try:
stirng = reader.GetMetaData(0, key).removesuffix(" ")
if stirng in ["No study description",
"No series description"]:
return None
else:
return stirng
except:
return None
study_description = get_meta("0008|1030")
series_description = get_meta("0008|103e")
series_modality = get_meta("0008|0060")
name = study_description or dir_path.name
if series_description and series_modality:
description = f"{series_description}-{series_modality}"
elif series_description:
description = series_description
elif series_modality:
description = series_modality
else:
description = ""
name = name.replace(" ", "-")
description = description.replace(" ", "-")
elif ext in SEQUENCE_EXTS:
itk_volume = sitk.ReadImage(sequence)
name = get_sequence_name(filepath).replace(" ", "-")
description = ""
else:
itk_volume = sitk.ReadImage(filepath)
name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
description = ""
# for key in itk_volume.GetMetaDataKeys():
# print(f"{key},{itk_volume.GetMetaData(key)}")
if progress_callback:
progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
if not progressing:
raise CancelledByUser
if itk_volume.GetDimension() == 3:
itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
volume = sitk.GetArrayFromImage(itk_volume)
# transpose ijk to kji
if volume.ndim == 4:
volume = np.transpose(volume, (2, 1, 0, 3))
else:
volume = np.transpose(volume)
volume = np.expand_dims(volume, axis=-1) # expend channel
volume = np.expand_dims(volume, axis=0) # expend frame
meta = {
"name": name,
"description": description,
"shape": tuple(itk_volume.GetSize()),
"spacing": tuple(itk_volume.GetSpacing()),
"origin": tuple(itk_volume.GetOrigin()),
"direction": tuple(itk_volume.GetDirection()),
"frame_count": volume.shape[0],
"channel_count": volume.shape[-1],
"is_oriented": True
}
if itk_volume.GetDimension() == 4:
# FIXME: not sure...
direction = np.array(itk_volume.GetDirection())
direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \
else direction.reshape(4, 4)
direction = direction[1:, 1:]
direction = tuple(direction.flatten())
volume = sitk.GetArrayFromImage(itk_volume)
if volume.ndim == 5:
volume = np.transpose(volume, (0, 3, 2, 1, 4))
else:
volume = np.transpose(volume, (0, 3, 2, 1))
volume = np.expand_dims(volume, axis=-1)
meta = {
"name": name,
"description": description,
"shape": tuple(itk_volume.GetSize()[:3]),
"spacing": tuple(itk_volume.GetSpacing()[:3]),
"origin": tuple(itk_volume.GetOrigin()[:3]),
"direction": direction,
"frame_count": volume.shape[0],
"channel_count": volume.shape[-1],
"is_oriented": False
}
return volume, meta

4
bioxelnodes/requirements.txt
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@@ -1 +1,3 @@
SimpleITK==2.3.1 # Insight Segmentation and Registration Toolkit.
SimpleITK==2.3.1 # Insight Segmentation and Registration Toolkit.
pyometiff==1.0.0 # .ome.tiff
mrcfile==1.5.1 # .map

19
bioxelnodes/utils.py
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@@ -72,12 +72,19 @@ def get_nodes_by_type(node_group, type_name: str):
return [node for node in node_group.nodes if get_node_type(node) == type_name]
def show_message(message="", title="Message Box", icon='INFO'):
def progress_bar(self, context):
row = self.layout.row()
row.progress(
factor=context.window_manager.bioxelnodes_progress_factor,
type="BAR",
text=context.window_manager.bioxelnodes_progress_text
)
row.scale_x = 2
def draw(self, context):
self.layout.label(text=message)
bpy.context.window_manager.popup_menu(draw, title=title, icon=icon)
def progress_update(context, factor, text=""):
context.window_manager.bioxelnodes_progress_factor = factor
context.window_manager.bioxelnodes_progress_text = text
def calc_bbox_verts(origin, size):
@@ -157,7 +164,7 @@ def save_vdb(grids, context):
cache_dir.mkdir(parents=True, exist_ok=True)
vdb_path = Path(cache_dir, f"{uuid4()}.vdb")
print(f"Storing the VDB file ({str(vdb_path)})...")
# print(f"Storing the VDB file ({str(vdb_path)})...")
vdb.write(str(vdb_path), grids=grids)
return vdb_path
@@ -174,7 +181,7 @@ def save_vdbs(grids_sequence, context):
vdb_paths = []
for f, grids in enumerate(grids_sequence):
vdb_path = Path(vdb_dir_path, f"{vdb_name}.{str(f+1).zfill(4)}.vdb")
print(f"Storing the VDB file ({str(vdb_path)})...")
# print(f"Storing the VDB file ({str(vdb_path)})...")
vdb.write(str(vdb_path), grids=grids)
vdb_paths.append(vdb_path)