Merge pull request #29 from OmooLab/feature/dev

feat: support more format
2024-07-22 08:51:59 +08:00 · 2024-07-22 08:51:12 +08:00
15 changed files with 1407 additions and 704 deletions
--- a/.github/workflows/upload-assets.yml
+++ b/.github/workflows/upload-assets.yml
@@ -88,7 +88,15 @@ jobs:
          python-version: 3.11
      - name: Zip Extension
        run: |
-          pip download SimpleITK==2.3.1 --dest bioxelnodes/wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download SimpleITK==2.3.1 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download pyometiff==1.0.0 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          pip download mrcfile==1.5.1 --dest wheels --only-binary=:all: --python-version=3.11 --platform=win_amd64
+          mkdir bioxelnodes/wheels
+          cp wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl bioxelnodes/wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl
+          cp wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl bioxelnodes/wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl
+          cp wheels/tifffile-2024.7.21-py3-none-any.whl bioxelnodes/wheels/tifffile-2024.7.21-py3-none-any.whl
+          cp wheels/pyometiff-1.0.0-py3-none-any.whl bioxelnodes/wheels/pyometiff-1.0.0-py3-none-any.whl
+          cp wheels/mrcfile-1.5.1-py2.py3-none-any.whl bioxelnodes/wheels/mrcfile-1.5.1-py2.py3-none-any.whl
          rm -r bioxelnodes/externalpackage
          cp extension/__init__.py bioxelnodes/__init__.py
          cp extension/preferences.py bioxelnodes/preferences.py
--- a/bioxelnodes/init.py
+++ b/bioxelnodes/init.py
@@ -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()


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


--- a/bioxelnodes/operators.py
+++ b/bioxelnodes/operators.py
@@ -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'}

--- a/bioxelnodes/parse.py
+++ b/bioxelnodes/parse.py
@@ -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
--- a/bioxelnodes/requirements.txt
+++ b/bioxelnodes/requirements.txt
@@ -1 +1,3 @@
 SimpleITK==2.3.1     # Insight Segmentation and Registration Toolkit.
+pyometiff==1.0.0     # .ome.tiff
+mrcfile==1.5.1       # .map
--- a/bioxelnodes/utils.py
+++ b/bioxelnodes/utils.py
@@ -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)

--- a/extension/init.py
+++ b/extension/init.py
@@ -9,6 +9,8 @@ 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()


--- a/extension/blender_manifest.toml
+++ b/extension/blender_manifest.toml
@@ -3,7 +3,7 @@ schema_version = "1.0.0"
 # Example of manifest file for a Blender extension
 # Change the values according to your extension
 id = "bioxelnodes"
-version = "0.2.7"
+version = "0.2.8"
 name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Ma Nan <icrdr2010@outlook.com>"
@@ -15,7 +15,7 @@ website = "https://omoolab.github.io/BioxelNodes/latest"

 # Optional list defined by Blender and server, see:
 # https://docs.blender.org/manual/en/dev/advanced/extensions/tags.html
-tags = ["Geometry Nodes", "Render"]
+tags = ["Geometry Nodes", "Render", "Import-Export"]

 blender_version_min = "4.2.0"
 # Optional: maximum supported Blender version
@@ -38,7 +38,11 @@ platforms = ["windows-x64"]
 # Optional: bundle 3rd party Python modules.
 # https://docs.blender.org/manual/en/dev/advanced/extensions/python_wheels.html
 wheels = [
-  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl"
+  "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl",
+  "./wheels/lxml-5.2.2-cp311-cp311-win_amd64.whl",
+  "./wheels/tifffile-2024.7.21-py3-none-any.whl",
+  "./wheels/pyometiff-1.0.0-py3-none-any.whl",
+  "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl"
 ]


--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -13,7 +13,7 @@ nav:
      - Prepare Your Data: prepare_data.md
      - Step by Step: step_by_step.md
      - Concepts & Pipeline: concept.md
-  - Visualizating any Bio-structure:
+  - Visualizing any Bio-structure:
      - Import & Preprocess: import.md
      - Mask Methods: mask.md
      - Assgin a Shader: shader.md
--- a/poetry.lock
+++ b/poetry.lock
@@ -539,6 +539,49 @@ files = [
    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]

+[[package]]
+name = "imagecodecs"
+version = "2024.6.1"
+description = "Image transformation, compression, and decompression codecs"
+optional = false
+python-versions = ">=3.9"
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+]
+
+[package.dependencies]
+numpy = "*"
+
+[package.extras]
+all = ["matplotlib", "numcodecs", "tifffile"]
+
 [[package]]
 name = "imageio"
 version = "2.34.2"
@@ -784,6 +827,164 @@ dev = ["changelist (==0.5)"]
 lint = ["pre-commit (==3.7.0)"]
 test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]

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+files = [
+    {file = "pyometiff-1.0.0-py3-none-any.whl", hash = "sha256:6c274786f32b9bd662105af37419c7f2f7ee6194bc1a7283b4ab2a00c53cf632"},
+    {file = "pyometiff-1.0.0.tar.gz", hash = "sha256:596b7a7377a5f2e50292aa52dd22e6347a2d2f21577e93d1fcdcd63942e597f7"},
+]
+
+[package.dependencies]
+imagecodecs = "*"
+lxml = "*"
+numpy = "*"
+tifffile = ">2020.10.1"
+
+[package.extras]
+dev = ["mock", "pytest (>3.7)"]
+
 [[package]]
 name = "pyparsing"
 version = "3.1.2"
@@ -2225,4 +2460,4 @@ cffi = ["cffi (>=1.11)"]
 [metadata]
 lock-version = "2.0"
 python-versions = "~=3.10.0"
-content-hash = "e9980867106af8e9e7524ff319d3c0785906b359022595732260fd4b3ca135ca"
+content-hash = "5eb6cfca92f09b1f4bba15042adc44cafa174f28d7b4520bde92f0f7235fd233"
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioxelnodes"
-version = "0.2.7"
+version = "0.2.8"
 description = ""
 authors = ["Ma Nan <icrdr2010@outlook.com>"]
 license = "MIT"
@@ -11,6 +11,8 @@ python = "~=3.10.0"
 bpy = "~=4.0"
 simpleitk = "^2.3.1"
 scikit-image = "^0.24.0"
+pyometiff = "^1.0.0"
+mrcfile = "^1.5.1"

 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.25.2"
Author	SHA1	Message	Date
Ma Nan	b6e7ae0c8b	Merge pull request #29 from OmooLab/feature/dev feat: support more format	2024-07-22 08:51:59 +08:00
Ma Nan	854af4c3bc	feat: support more format feat: support .mrc .map feat: support .ome.tif feat: improved user experience for importing feat: better contrast algorithm	2024-07-22 08:51:12 +08:00