MHD#

IO interface to mhd / raw files.

Note

Using the function write_header_from_source() a mhd header for a numpy binary array can be created to enable loading the numpy file into imagej.

class Source(location, name=None)[source]#

Bases: Source

Mhd/raw array source.

as_array()[source]#

as_buffer()[source]#

as_memmap()[source]#

as_real()[source]#

as_virtual()[source]#

Return virtual source without array data to pass in parallel processing.

Returns

sourceSource class: The source class without array data.

metadata(info=None)[source]#

Returns metadata from this mhd file.

Arguments

infolist or all: Optional list of keywords, if all return full tif metadata, if None return default set info.

Returns

metadatadict: Dictionary with the metadata.

property array#

The underlying data array.

Returns

arrayarray: The underlying data array of this source.

property dtype#

The data type of the source.

Returns

dtypedtype: The data type of the source.

property element_strides#

The strides of the array elements.

Returns

stridestuple: Strides of the array elements.

Note

The strides of the elements module itemsize instead of bytes.

property location#

The location where the data of the source is stored.

Returns

locationstr or None: Returns the location of the data source or None if this source lives in memory only.

property name#

The name of this source.

Returns

namestr: Name of this source.

property offset#

The offset of the memory map in the file.

Returns

offsetint: Offset of the memory map in the file.

property order#

The order of how the data is stored in the source.

Returns

orderstr: Returns ‘C’ for C contiguous and ‘F’ for fortran contiguous, None otherwise.

property shape#

The shape of the source.

Returns

shapetuple: The shape of the source.

class VirtualSource(source=None, shape=None, dtype=None, order=None, location=None, name=None)[source]#

Bases: VirtualSource

as_buffer()[source]#

as_real()[source]#

as_virtual()[source]#

Return virtual source without array data to pass in parallel processing.

Returns

sourceSource class: The source class without array data.

property name#

The name of this source.

Returns

namestr: Name of this source.

create(location=None, shape=None, dtype=None, array=None, as_source=True, **kwargs)[source]#

header_from_source(source=None, location=None, header=None, return_header_and_raw_file=False)[source]#

Create a mhd header dictionary for a source.

Arguments

sourceSource specification: Source file or class to create a mhd header file for.
locationstr or None: Location of the mhd file. If None, the source location with extension ‘mhd’ is used.
headerdict or None: Optional additional entries for the header file.
return_header_and_raw_filebool: If True also return the header file.

Returns

headerdict: The mhd header dictionary.

Note

This function can be used to make npy files readable in image processing software tools that allow to import mhd files, such ash ImageJ.

is_mhd(source)[source]#: Checks if this source is an MHD source.

read(source, slicing=None, **kwargs)[source]#

Read data from a mhd file.

Arguments

sourcestr: The name of the mhd file.
slicingslice, Slice or None: An optional sub-slice to consider.

Returns

arrayarray: The image data in the tif file as a buffer.

write(sink, data, slicing=None, **kwargs)[source]#: Write specialization for mhd files.

write_header_from_source(source, location=None, header=None)[source]#

Create a mhd header file for a source file.

Arguments

sourceSource specification: Source file or class to create a mhd header file for.
locationstr or None: Location of the mhd file. If None, the source location with extension ‘mhd’ is used.
headerdict or None: Optional additional entries for the header file.

Returns

filenamestr: The filename of the mhd header.