Ma Nan
854af4c3bc
feat: support .mrc .map feat: support .ome.tif feat: improved user experience for importing feat: better contrast algorithm
370 lines
13 KiB
Python
370 lines
13 KiB
Python
from pathlib import Path
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import numpy as np
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from .exceptions import CancelledByUser
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from .utils import get_text_index_str
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try:
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import SimpleITK as sitk
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from pyometiff import OMETIFFReader
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import mrcfile
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except:
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...
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SUPPORT_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
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'.bmp', '.BMP',
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'.PIC', '.pic',
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'.gipl', '.gipl.gz',
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'.jpg', '.JPG', '.jpeg', '.JPEG',
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'.lsm', '.LSM',
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'.tif', '.TIF', '.tiff', '.TIFF',
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'.mnc', '.MNC',
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'.mrc', '.rec',
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'.mha', '.mhd',
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'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
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'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
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'.nrrd', '.nhdr',
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'.png', '.PNG',
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'.vtk',
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'.ome.tiff', '.ome.tif',
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'.mrc', '.mrc.gz', '.map', '.map.gz']
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OME_EXTS = ['.ome.tiff', '.ome.tif',
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'.tif', '.TIF', '.tiff', '.TIFF']
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MRC_EXTS = ['.mrc', '.mrc.gz', '.map', '.map.gz']
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SEQUENCE_EXTS = ['.bmp', '.BMP',
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'.jpg', '.JPG', '.jpeg', '.JPEG',
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'.tif', '.TIF', '.tiff', '.TIFF',
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'.png', '.PNG']
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DICOM_EXTS = ['', '.dcm', '.DCM', '.DICOM']
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FH_EXTS = ['', '.dcm', '.DCM', '.DICOM', '.ima', '.IMA',
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'.gipl', '.gipl.gz',
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'.mnc', '.MNC',
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'.mrc', '.rec',
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'.mha', '.mhd',
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'.nia', '.nii', '.nii.gz', '.hdr', '.img', '.img.gz',
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'.hdf', '.h4', '.hdf4', '.he2', '.h5', '.hdf5', '.he5',
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'.nrrd', '.nhdr',
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'.vtk',
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'.gz']
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def get_ext(filepath: str) -> str:
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file_path = Path(filepath)
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if file_path.name.endswith(".nii.gz"):
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return ".nii.gz"
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elif file_path.name.endswith(".img.gz"):
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return ".img.gz"
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elif file_path.name.endswith(".gipl.gz"):
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return ".gipl.gz"
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elif file_path.name.endswith(".ome.tiff"):
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return ".ome.tiff"
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elif file_path.name.endswith(".ome.tif"):
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return ".ome.tif"
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elif file_path.name.endswith(".mrc.gz"):
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return ".mrc.gz"
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elif file_path.name.endswith(".map.gz"):
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return ".map.gz"
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else:
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return file_path.suffix
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def get_sequence_name(filepath: str) -> str:
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ext = get_ext(filepath)
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filename = Path(filepath).name.removesuffix(ext)
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index: str = get_text_index_str(filename)
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return filename.removesuffix(index)
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def get_sequence_index(filepath: str) -> int:
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ext = get_ext(filepath)
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filename = Path(filepath).name.removesuffix(ext)
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index: str = get_text_index_str(filename)
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return int(index) if index else 0
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def collect_sequence(filepath: str):
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file_path = Path(filepath).resolve()
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files = list(file_path.parent.iterdir())
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file_dict = {}
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for file in files:
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if file.is_file() \
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and get_ext(file_path) == get_ext(file) \
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and get_sequence_name(file_path) == get_sequence_name(file):
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file_dict[get_sequence_index(file)] = file
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for key in file_dict.copy().keys():
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if not file_dict.get(key+1) \
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and not file_dict.get(key-1):
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del file_dict[key]
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file_dict = dict(sorted(file_dict.items()))
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sequence = [str(f) for f in file_dict.values()]
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if len(sequence) == 0:
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sequence = [str(file_path)]
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return sequence
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def parse_volumetric_data(filepath: str, series_id="", progress_callback=None):
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"""Parse any volumetric data to numpy with shap (T,X,Y,Z,C)
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Args:
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filepath (str): file path
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series_id (str, optional): DICOM series id. Defaults to "".
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Returns:
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_type_: _description_
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"""
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ext = get_ext(filepath)
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if progress_callback:
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progressing = progress_callback(0, "Reading the Data...")
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if not progressing:
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raise CancelledByUser
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is_sequence = False
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if ext in SEQUENCE_EXTS:
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sequence = collect_sequence(filepath)
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if len(sequence) > 1:
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is_sequence = True
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if ext in MRC_EXTS and not is_sequence:
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# TODO: much to do with mrc
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with mrcfile.open(filepath) as mrc:
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volume = mrc.data
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# mrc.print_header()
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# print(volume.shape)
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# print(mrc.voxel_size)
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if mrc.is_single_image():
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volume = np.expand_dims(volume, axis=0) # expend frame
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volume = np.expand_dims(volume, axis=-1) # expend Z
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volume = np.expand_dims(volume, axis=-1) # expend channel
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elif mrc.is_image_stack():
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volume = np.expand_dims(volume, axis=-1) # expend Z
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volume = np.expand_dims(volume, axis=-1) # expend channel
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elif mrc.is_volume():
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volume = np.expand_dims(volume, axis=0) # expend frame
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volume = np.expand_dims(volume, axis=-1) # expend channel
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elif mrc.is_volume_stack():
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volume = np.expand_dims(volume, axis=-1) # expend channel
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name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
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shape = volume.shape[1:4]
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spacing = (mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z)
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meta = {
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"name": name,
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"description": "",
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"shape": shape,
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"spacing": spacing,
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"origin": (0, 0, 0),
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"direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
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"frame_count": volume.shape[0],
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"channel_count": volume.shape[-1],
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"is_oriented": False
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}
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elif ext in OME_EXTS and not is_sequence:
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reader = OMETIFFReader(fpath=filepath)
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ome_volume, metadata, xml_metadata = reader.read()
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if progress_callback:
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progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
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if not progressing:
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raise CancelledByUser
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try:
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# print(ome_volume.shape)
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# for key in metadata:
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# print(f"{key},{metadata[key]}")
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ome_order = metadata['DimOrder BF Array']
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except:
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ome_order = "TCZYX"
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if ome_volume.ndim == 2:
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ome_order = ome_order.replace("T", "")\
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.replace("C", "").replace("Z", "")
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bioxel_order = (ome_order.index('X'),
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ome_order.index('Y'))
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volume = np.transpose(ome_volume, bioxel_order)
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volume = np.expand_dims(volume, axis=0) # expend frame
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volume = np.expand_dims(volume, axis=-1) # expend Z
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volume = np.expand_dims(volume, axis=-1) # expend channel
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elif ome_volume.ndim == 3:
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# -> XYZC
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ome_order = ome_order.replace("T", "").replace("C", "")
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bioxel_order = (ome_order.index('X'),
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ome_order.index('Y'),
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ome_order.index('Z'))
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volume = np.transpose(ome_volume, bioxel_order)
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volume = np.expand_dims(volume, axis=0) # expend frame
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volume = np.expand_dims(volume, axis=-1) # expend channel
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elif ome_volume.ndim == 4:
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# -> XYZC
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ome_order = ome_order.replace("T", "")
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bioxel_order = (ome_order.index('X'),
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ome_order.index('Y'),
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ome_order.index('Z'),
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ome_order.index('C'))
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volume = np.transpose(ome_volume, bioxel_order)
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volume = np.expand_dims(volume, axis=0) # expend frame
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elif ome_volume.ndim == 5:
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# -> TXYZC
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bioxel_order = (ome_order.index('T'),
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ome_order.index('X'),
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ome_order.index('Y'),
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ome_order.index('Z'),
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ome_order.index('C'))
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volume = np.transpose(ome_volume, bioxel_order)
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shape = volume.shape[1:4]
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try:
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spacing = (metadata['PhysicalSizeX'],
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metadata['PhysicalSizeY'],
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metadata['PhysicalSizeZ'])
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except:
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spacing = (1, 1, 1)
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name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
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meta = {
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"name": name,
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"description": "",
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"shape": shape,
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"spacing": spacing,
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"origin": (0, 0, 0),
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"direction": (1, 0, 0, 0, 1, 0, 0, 0, 1),
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"frame_count": volume.shape[0],
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"channel_count": volume.shape[-1],
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"is_oriented": False
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}
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else:
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if ext in DICOM_EXTS:
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dir_path = Path(filepath).resolve().parent
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reader = sitk.ImageSeriesReader()
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reader.MetaDataDictionaryArrayUpdateOn()
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reader.LoadPrivateTagsOn()
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series_files = reader.GetGDCMSeriesFileNames(
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str(dir_path), series_id)
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reader.SetFileNames(series_files)
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itk_volume = reader.Execute()
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# for k in reader.GetMetaDataKeys(0):
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# v = reader.GetMetaData(0, k)
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# print(f'({k}) = = "{v}"')
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def get_meta(key):
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try:
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stirng = reader.GetMetaData(0, key).removesuffix(" ")
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if stirng in ["No study description",
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"No series description"]:
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return None
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else:
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return stirng
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except:
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return None
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study_description = get_meta("0008|1030")
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series_description = get_meta("0008|103e")
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series_modality = get_meta("0008|0060")
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name = study_description or dir_path.name
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if series_description and series_modality:
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description = f"{series_description}-{series_modality}"
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elif series_description:
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description = series_description
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elif series_modality:
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description = series_modality
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else:
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description = ""
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name = name.replace(" ", "-")
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description = description.replace(" ", "-")
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elif ext in SEQUENCE_EXTS:
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itk_volume = sitk.ReadImage(sequence)
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name = get_sequence_name(filepath).replace(" ", "-")
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description = ""
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else:
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itk_volume = sitk.ReadImage(filepath)
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name = Path(filepath).name.removesuffix(ext).replace(" ", "-")
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description = ""
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# for key in itk_volume.GetMetaDataKeys():
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# print(f"{key},{itk_volume.GetMetaData(key)}")
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if progress_callback:
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progressing = progress_callback(0.5, "Transpose to 'TXYZC'...")
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if not progressing:
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raise CancelledByUser
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if itk_volume.GetDimension() == 3:
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itk_volume = sitk.DICOMOrient(itk_volume, 'RAS')
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volume = sitk.GetArrayFromImage(itk_volume)
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# transpose ijk to kji
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if volume.ndim == 4:
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volume = np.transpose(volume, (2, 1, 0, 3))
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else:
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volume = np.transpose(volume)
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volume = np.expand_dims(volume, axis=-1) # expend channel
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volume = np.expand_dims(volume, axis=0) # expend frame
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meta = {
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"name": name,
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"description": description,
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"shape": tuple(itk_volume.GetSize()),
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"spacing": tuple(itk_volume.GetSpacing()),
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"origin": tuple(itk_volume.GetOrigin()),
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"direction": tuple(itk_volume.GetDirection()),
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"frame_count": volume.shape[0],
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"channel_count": volume.shape[-1],
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"is_oriented": True
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}
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if itk_volume.GetDimension() == 4:
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# FIXME: not sure...
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direction = np.array(itk_volume.GetDirection())
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direction = direction.reshape(3, 3) if itk_volume.GetDimension() == 3 \
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else direction.reshape(4, 4)
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direction = direction[1:, 1:]
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direction = tuple(direction.flatten())
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volume = sitk.GetArrayFromImage(itk_volume)
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if volume.ndim == 5:
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volume = np.transpose(volume, (0, 3, 2, 1, 4))
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else:
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volume = np.transpose(volume, (0, 3, 2, 1))
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volume = np.expand_dims(volume, axis=-1)
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meta = {
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"name": name,
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"description": description,
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"shape": tuple(itk_volume.GetSize()[:3]),
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"spacing": tuple(itk_volume.GetSpacing()[:3]),
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"origin": tuple(itk_volume.GetOrigin()[:3]),
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"direction": direction,
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"frame_count": volume.shape[0],
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"channel_count": volume.shape[-1],
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"is_oriented": False
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}
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return volume, meta
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