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_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_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.
- 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.
- 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_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.