# Original Version: bjian 2008/10/27
# 3-D extension: PJackson 2013/06/06
# More datatypes, Multiple Channels, Python 3, ...: Peter Fischer
from __future__ import division, print_function
from typing import Dict, Tuple, Any
from os import PathLike
import sys
from pathlib import Path
import numpy as np
def read_meta_header(filename: PathLike) -> Dict[str, Any]:
"""
Return a dictionary of meta data from MHD meta header file
:param filename: file of type .mhd that should be loaded
:returns: dictionary of meta data
"""
# Define tags
meta_dict = {}
tag_set = []
tag_set.extend(['ObjectType', 'NDims', 'DimSize', 'ElementType', 'ElementDataFile', 'ElementNumberOfChannels'])
tag_set.extend(['BinaryData', 'BinaryDataByteOrderMSB', 'CompressedData', 'CompressedDataSize'])
tag_set.extend(['Offset', 'CenterOfRotation', 'AnatomicalOrientation', 'ElementSpacing', 'TransformMatrix'])
tag_set.extend(['Comment', 'SeriesDescription', 'AcquisitionDate', 'AcquisitionTime', 'StudyDate', 'StudyTime'])
tag_flag = [False] * len(tag_set)
with open(filename, "r") as fn:
line = fn.readline()
while line:
tags = str.split(line, '=')
# print(tags[0])
for i in range(len(tag_set)):
tag = tag_set[i]
if (str.strip(tags[0]) == tag) and (not tag_flag[i]):
# print(tags[1])
content = str.strip(tags[1])
if tag in ['ElementSpacing', 'Offset', 'CenterOfRotation', 'TransformMatrix']:
meta_dict[tag] = [float(s) for s in content.split()]
elif tag in ['NDims', 'ElementNumberOfChannels']:
meta_dict[tag] = int(content)
elif tag in ['DimSize']:
meta_dict[tag] = [int(s) for s in content.split()]
elif tag in ['BinaryData', 'BinaryDataByteOrderMSB', 'CompressedData']:
if content == "True":
meta_dict[tag] = True
else:
meta_dict[tag] = False
else:
meta_dict[tag] = content
tag_flag[i] = True
line = fn.readline()
return meta_dict
def load_raw_data_with_mhd(filename: PathLike) -> Tuple[np.ndarray, Dict[str, Any]]:
"""
Load a MHD file
:param filename: file of type .mhd that should be loaded
:returns: tuple with raw data and dictionary of meta data
"""
meta_dict = read_meta_header(filename)
dim = int(meta_dict['NDims'])
if "ElementNumberOfChannels" in meta_dict:
element_channels = int(meta_dict["ElementNumberOfChannels"])
else:
element_channels = 1
if meta_dict['ElementType'] == 'MET_FLOAT':
np_type = np.float32
elif meta_dict['ElementType'] == 'MET_DOUBLE':
np_type = np.float64
elif meta_dict['ElementType'] == 'MET_CHAR':
np_type = np.byte
elif meta_dict['ElementType'] == 'MET_UCHAR':
np_type = np.ubyte
elif meta_dict['ElementType'] == 'MET_SHORT':
np_type = np.short
elif meta_dict['ElementType'] == 'MET_USHORT':
np_type = np.ushort
elif meta_dict['ElementType'] == 'MET_INT':
np_type = np.int32
elif meta_dict['ElementType'] == 'MET_UINT':
np_type = np.uint32
else:
raise NotImplementedError("ElementType " + meta_dict['ElementType'] + " not understood.")
arr = list(meta_dict['DimSize'])
volume = np.prod(arr[0:dim - 1])
pwd = Path(filename).parents[0].resolve()
data_file = Path(meta_dict['ElementDataFile'])
if not data_file.is_absolute():
data_file = pwd / data_file
shape = (arr[dim - 1], volume, element_channels)
with open(data_file,'rb') as f:
data = np.fromfile(f, count=np.prod(shape), dtype=np_type)
data.shape = shape
# Adjust byte order in numpy array to match default system byte order
if 'BinaryDataByteOrderMSB' in meta_dict:
sys_byteorder_msb = sys.byteorder == 'big'
file_byteorder_ms = meta_dict['BinaryDataByteOrderMSB']
if sys_byteorder_msb != file_byteorder_ms:
data = data.byteswap()
# Begin 3D fix
arr.reverse()
if element_channels > 1:
data = data.reshape(arr + [element_channels])
else:
data = data.reshape(arr)
# End 3D fix
return (data, meta_dict)
def write_meta_header(filename: PathLike, meta_dict: Dict[str, Any]):
"""
Write the MHD meta header file
:param filename: file to write
:param meta_dict: dictionary of meta data in MetaImage format
"""
header = ''
# do not use tags = meta_dict.keys() because the order of tags matters
tags = ['ObjectType', 'NDims', 'BinaryData',
'BinaryDataByteOrderMSB', 'CompressedData', 'CompressedDataSize',
'TransformMatrix', 'Offset', 'CenterOfRotation',
'AnatomicalOrientation', 'ElementSpacing',
'DimSize', 'ElementNumberOfChannels', 'ElementType', 'ElementDataFile',
'Comment', 'SeriesDescription', 'AcquisitionDate',
'AcquisitionTime', 'StudyDate', 'StudyTime']
for tag in tags:
if tag in meta_dict.keys():
header += '%s = %s\n' % (tag, meta_dict[tag])
with open(filename, 'w') as f:
f.write(header)
def write_mhd_file(filename: PathLike, data: np.ndarray, **meta_dict):
"""
Write a meta file and the raw file.
The byte order of the raw file will always be in the byte order of the system.
:param filename: file to write
:param meta_dict: dictionary of meta data in MetaImage format
"""
assert filename[-4:] == '.mhd'
meta_dict['ObjectType'] = 'Image'
meta_dict['BinaryData'] = 'True'
meta_dict['BinaryDataByteOrderMSB'] = 'False' if sys.byteorder == 'little' else 'True'
if data.dtype == np.float32:
meta_dict['ElementType'] = 'MET_FLOAT'
elif data.dtype == np.double or data.dtype == np.float64:
meta_dict['ElementType'] = 'MET_DOUBLE'
elif data.dtype == np.byte:
meta_dict['ElementType'] = 'MET_CHAR'
elif data.dtype == np.uint8 or data.dtype == np.ubyte:
meta_dict['ElementType'] = 'MET_UCHAR'
elif data.dtype == np.short or data.dtype == np.int16:
meta_dict['ElementType'] = 'MET_SHORT'
elif data.dtype == np.ushort or data.dtype == np.uint16:
meta_dict['ElementType'] = 'MET_USHORT'
elif data.dtype == np.int32:
meta_dict['ElementType'] = 'MET_INT'
elif data.dtype == np.uint32:
meta_dict['ElementType'] = 'MET_UINT'
else:
raise NotImplementedError("ElementType " + str(data.dtype) + " not implemented.")
dsize = list(data.shape)
if 'ElementNumberOfChannels' in meta_dict.keys():
element_channels = int(meta_dict['ElementNumberOfChannels'])
assert(dsize[-1] == element_channels)
dsize = dsize[:-1]
else:
element_channels = 1
dsize.reverse()
meta_dict['NDims'] = str(len(dsize))
meta_dict['DimSize'] = dsize
meta_dict['ElementDataFile'] = str(Path(filename).name).replace('.mhd', '.raw')
print(str(Path(filename).name).replace('.mhd', '.raw'))
# Tags that need conversion of list to string
tags = ['ElementSpacing', 'Offset', 'DimSize', 'CenterOfRotation', 'TransformMatrix']
for tag in tags:
if tag in meta_dict.keys() and not isinstance(meta_dict[tag], str):
meta_dict[tag] = ' '.join([str(i) for i in meta_dict[tag]])
write_meta_header(filename, meta_dict)
# Compute absolute path to write to
pwd = Path(filename).parents[0].resolve()
data_file = Path(meta_dict['ElementDataFile'])
if not data_file.is_absolute():
data_file = pwd / data_file
# Dump raw data
data = data.reshape(dsize[0], -1, element_channels)
with open(data_file, 'wb') as f:
data.tofile(f)
