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fix: io

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This commit is contained in:
马南
2024-05-13 12:09:11 +08:00
parent 1990a16972
commit 5e8d12c564
5 changed files with 183 additions and 97 deletions
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218
bioxelnodes/io.py
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@@ -7,7 +7,7 @@ from pathlib import Path
from uuid import uuid4
import mathutils
import math
from .utils import calc_bbox_verts, get_text_index, get_bioxels_obj, get_node_by_type, show_message
from .utils import calc_bbox_verts, get_text_index_str, get_bioxels_obj, get_node_by_type, show_message
from .nodes import custom_nodes
from .props import BIOXELNODES_Series
try:
@@ -52,30 +52,16 @@ FH_EXTS = ['.dcm', '.DICOM',
def get_bioxels_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple):
return (
math.ceil(orig_shape[0] / bioxel_size * orig_spacing[0]),
math.ceil(orig_shape[1] / bioxel_size * orig_spacing[1]),
math.ceil(orig_shape[2] / bioxel_size * orig_spacing[2]),
)
shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]),
int(orig_shape[1] / bioxel_size * orig_spacing[1]),
int(orig_shape[2] / bioxel_size * orig_spacing[2]))
return (shape[0] if shape[0] > 0 else 1,
shape[1] if shape[1] > 0 else 1,
shape[2] if shape[2] > 0 else 1)
def collect_image_sequence(filepath: str):
file_path = Path(filepath).resolve()
files = list(file_path.parent.iterdir())
files = [f for f in files if f.is_file()
and get_ext(file_path) == get_ext(f)
and get_text_index(f.stem)]
def get_index(f: Path):
return get_text_index(f.stem)
files.sort(key=get_index)
sequence = [str(f) for f in files]
return sequence
def get_ext(filepath: str):
def get_ext(filepath: str) -> str:
file_path = Path(filepath)
if file_path.name.endswith(".nii.gz"):
return ".nii.gz"
@@ -87,11 +73,38 @@ def get_ext(filepath: str):
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_image_sequence(filepath: str):
file_path = Path(filepath).resolve()
files = list(file_path.parent.iterdir())
files = [f for f in files if f.is_file()
and get_ext(file_path) == get_ext(f)
and get_sequence_name(file_path) == get_sequence_name(f)]
files.sort(key=get_sequence_index)
sequence = [str(f) for f in files]
return sequence
def read_image(filepath: str, series_id=""):
ext = get_ext(filepath)
dir_path = Path(filepath).resolve().parent
filename = Path(filepath).resolve().stem
if ext in DICOM_EXTS:
dir_path = Path(filepath).resolve().parent
reader = sitk.ImageSeriesReader()
reader.MetaDataDictionaryArrayUpdateOn()
reader.LoadPrivateTagsOn()
@@ -99,19 +112,36 @@ def read_image(filepath: str, series_id=""):
str(dir_path), series_id)
reader.SetFileNames(series_files)
image = reader.Execute()
elif ext in SEQUENCE_EXTS and get_text_index(filename):
sequence = collect_image_sequence(filepath)
image = sitk.ReadImage(sequence)
else:
name = dir_path.name
elif ext in SEQUENCE_EXTS:
image = sitk.ReadImage(filepath)
if image.GetDimension() == 2:
image = sitk.ReadImage([filepath])
sequence = collect_image_sequence(filepath)
image = sitk.ReadImage(sequence)
name = get_sequence_name(filepath)
else:
image = sitk.ReadImage(filepath)
name = Path(filepath).name.removesuffix(ext)
else:
image = sitk.ReadImage(filepath)
name = Path(filepath).name.removesuffix(ext)
return image
return image, name
class ImportImageDialog(bpy.types.Operator):
bl_idname = "bioxelnodes.import_image_dialog"
def rgb2gray(image):
# Convert sRGB image to gray scale and rescale results to [0,255]
channels = [sitk.VectorIndexSelectionCast(
image, i, sitk.sitkFloat32) for i in range(image.GetNumberOfComponentsPerPixel())]
# linear mapping
I = (0.2126*channels[0] + 0.7152*channels[1] + 0.0722*channels[2])
return sitk.Cast(I, sitk.sitkFloat32)
class ImportVolumeDataDialog(bpy.types.Operator):
bl_idname = "bioxelnodes.import_volume_data_dialog"
bl_label = "Volume Data as Bioxels"
bl_description = "Import Volume Data as Bioxels (VDB)"
bl_options = {'UNDO'}
@@ -123,10 +153,19 @@ class ImportImageDialog(bpy.types.Operator):
series_id: bpy.props.StringProperty() # type: ignore
resample_method: bpy.props.EnumProperty(
name="Resample Method",
default="linear",
items=[("linear", "Linear", ""),
("nearest_neighbor", "Nearest Neighbor", ""),
("gaussian", "Gaussian", "")]
) # type: ignore
read_as: bpy.props.EnumProperty(
name="Read as",
default="scalar",
items=[("scalar", "Scalar", ""), ("labels", "Labels", "")]
items=[("scalar", "Scalar", ""),
("labels", "Labels", "")]
) # type: ignore
label_index: bpy.props.IntProperty(
@@ -169,11 +208,7 @@ class ImportImageDialog(bpy.types.Operator):
) # type: ignore
def execute(self, context):
bioxels_name = Path(self.filepath).parent.name \
if get_ext(self.filepath) in SEQUENCE_EXTS \
else Path(self.filepath).name.removesuffix(get_ext(self.filepath))
image = read_image(self.filepath, self.series_id)
image, bioxels_name = read_image(self.filepath, self.series_id)
bioxel_size = self.bioxel_size
orig_spacing = self.orig_spacing
@@ -189,16 +224,37 @@ class ImportImageDialog(bpy.types.Operator):
bioxels_shape = get_bioxels_shape(
bioxel_size, image_shape, orig_spacing)
print("Resampling...")
if self.read_as == "labels":
image = sitk.Cast(image, sitk.sitkUInt16)
default_value = 0
elif self.read_as == "scalar":
if "vector" in image.GetPixelIDTypeAsString():
print("Convet to Grayscale...")
image = rgb2gray(image)
else:
image = sitk.Cast(image, sitk.sitkFloat32)
stats = sitk.StatisticsImageFilter()
stats.Execute(image)
default_value = stats.GetMaximum() if self.invert_scalar else stats.GetMinimum()
if self.resample_method == "linear":
interpolator = sitk.sitkLinear
elif self.resample_method == "nearest_neighbor":
interpolator = sitk.sitkNearestNeighbor
elif self.resample_method == "gaussian":
interpolator = sitk.sitkGaussian
print(f"Resampling...")
image = sitk.Resample(
image1=image,
size=bioxels_shape,
transform=sitk.Transform(),
interpolator=sitk.sitkLinear,
interpolator=interpolator,
outputOrigin=image.GetOrigin(),
outputSpacing=bioxels_spacing,
outputDirection=image.GetDirection(),
defaultPixelValue=0,
defaultPixelValue=default_value,
outputPixelType=image.GetPixelID(),
)
@@ -219,17 +275,20 @@ class ImportImageDialog(bpy.types.Operator):
# A (nterior) j -> j -> y
# S (uperior) k -> i -> z
array = sitk.GetArrayFromImage(image)
array = np.transpose(array)
orig_dtype = str(array.dtype)
# print(f"Coverting Dtype from {orig_dtype} to float...")
# array = array.astype(float)
if array.ndim == 4:
if array.shape[3] == 3 and self.read_as == "scalar":
# RGB -> Grayscale
array = np.dot(array[..., :3], [0.2989, 0.5870, 0.1140])
else:
array = array[:, :, :, 0]
# if array.shape[0] == 3 and self.read_as == "scalar":
# # RGB -> Grayscale
# array = np.dot(array[..., :3], [0.2989, 0.5870, 0.1140])
# else:
# array = array[:, :, :, 0]
array = array[:, :, :, 0]
array = np.transpose(array)
bioxels_shape = array.shape
bioxels_offset = 0.0
@@ -260,16 +319,14 @@ class ImportImageDialog(bpy.types.Operator):
bioxels_max = float(np.max(array))
bioxels_min = float(np.min(array))
stat_table = [("Max", orig_max),
("Min", orig_min),
("Median", orig_median),
("Percentile 80%", orig_percentile80),
("Max (Offset)", bioxels_max),
("Min (Offset)", bioxels_min)]
stats_table = [("Max", orig_max),
("Min", orig_min),
("Median", orig_median),
("80%", orig_percentile80)]
print("Bioxels Value Stat: Max:")
for stat in stat_table:
print("| {: >20} | {: >20} |".format(*stat))
print("Bioxels Value Stats:")
for stats in stats_table:
print("| {: >10} | {: >40} |".format(*stats))
# # Build VDB
grid = vdb.BoolGrid() if self.read_as == "labels" else vdb.FloatGrid()
@@ -436,6 +493,7 @@ class ImportImageDialog(bpy.types.Operator):
text += "**TOO LARGE!**"
panel = layout.box()
panel.prop(self, "resample_method")
panel.prop(self, "bioxel_size")
row = panel.row()
row.prop(self, "orig_spacing")
@@ -472,9 +530,8 @@ class ReadDICOM(bpy.types.Operator):
bl_description = "Import Volume Data as Bioxels (VDB)"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(
subtype="FILE_PATH"
) # type: ignore
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
series_id: bpy.props.EnumProperty(
name="Select Series",
@@ -490,20 +547,27 @@ class ReadDICOM(bpy.types.Operator):
self.report({"WARNING"}, "Not supported extension.")
return {'CANCELLED'}
image = read_image(self.filepath, self.series_id)
print("Collecting Meta Data...")
print("Original Shape:", image.GetSize())
print("Original Spacing:", image.GetSpacing())
print("Original Origin:", image.GetOrigin())
print("Original Direction:", image.GetDirection())
image, name = read_image(self.filepath, self.series_id)
stats_table = [("Shape", str(image.GetSize())),
("Spacing", str(image.GetSpacing())),
("Origin", str(image.GetOrigin())),
("Direction", str(image.GetDirection())),
("Data Type", image.GetPixelIDTypeAsString())]
bpy.ops.bioxelnodes.import_image_dialog(
print("Meta Data:")
for stats in stats_table:
print("| {: >10} | {: >40} |".format(*stats))
do_orient = ext not in SEQUENCE_EXTS or ext in DICOM_EXTS
bpy.ops.bioxelnodes.import_volume_data_dialog(
'INVOKE_DEFAULT',
filepath=self.filepath,
orig_shape=image.GetSize(),
orig_spacing=image.GetSpacing(),
series_id=self.series_id or ""
series_id=self.series_id or "",
do_orient=do_orient
)
self.report({"INFO"}, "Successfully Readed.")
@@ -515,7 +579,7 @@ class ReadDICOM(bpy.types.Operator):
return {'FINISHED'}
def invoke(self, context, event):
if not self.filepath:
if not self.filepath and not self.directory:
return {'CANCELLED'}
show_message('Reading image data, it may take a while...',
@@ -551,20 +615,20 @@ class ReadDICOM(bpy.types.Operator):
text="Please be patient...")
class ImportImage(bpy.types.Operator):
bl_idname = "bioxelnodes.import_image"
class ImportVolumeData(bpy.types.Operator):
bl_idname = "bioxelnodes.import_volume_data"
bl_label = "Volume Data as Bioxels"
bl_description = "Import Volume Data as Bioxels (VDB)"
bl_options = {'UNDO'}
filepath: bpy.props.StringProperty(
subtype="FILE_PATH"
) # type: ignore
filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore
directory: bpy.props.StringProperty(subtype='DIR_PATH') # type: ignore
def execute(self, context):
bpy.ops.bioxelnodes.read_dicom(
'INVOKE_DEFAULT',
filepath=self.filepath
filepath=self.filepath,
directory=self.directory
)
return {'FINISHED'}
@@ -574,8 +638,8 @@ class ImportImage(bpy.types.Operator):
try:
class BIOXELNODES_FH_ImportImage(bpy.types.FileHandler):
bl_idname = "BIOXELNODES_FH_ImportImage"
class BIOXELNODES_FH_ImportVolumeData(bpy.types.FileHandler):
bl_idname = "BIOXELNODES_FH_ImportVolumeData"
bl_label = "File handler for dicom import"
bl_import_operator = "bioxelnodes.read_dicom"
bl_file_extensions = ";".join(FH_EXTS)