dm4 1.0.3.post1

Pure Python reader for Gatan Digital Micrograph 4 (DM4) files, providing access to image data and hierarchical metadata tags used in transmission electron microscopy.

dm4

A pure python file reader for Digital Micrograph’s DM4 file format

This package would not have been possible without the documentation provided by Dr Chris Boothroyd at http://www.er-c.org/cbb/info/dmformat/ Thank you.

Installation

Install using pip from the command line:

pip install dm4

Example

Below is a short example of reading the image data from a dm4 file. A more complete example can be found in the tests.:

import dm4
import PIL

input_path = "your_filename_here.dm4"

with dm4.DM4File.open(input_path) as dm4file:
    tags = dm4file.read_directory()

    image_data_tag = tags.named_subdirs['ImageList'].unnamed_subdirs[1].named_subdirs['ImageData']
    image_tag = image_data_tag.named_tags['Data']

    XDim = dm4file.read_tag_data(image_data_tag.named_subdirs['Dimensions'].unnamed_tags[0])
    YDim = dm4file.read_tag_data(image_data_tag.named_subdirs['Dimensions'].unnamed_tags[1])

    image_array = np.array(dm4file.read_tag_data(image_tag), dtype=np.uint16)
    image_array = np.reshape(image_array, (YDim, XDim))

    output_fullpath = "sample.tif"
    image = PIL.Image.fromarray(image_array, 'I;16')
    image.save(output_fullpath)

Script usage

The dm4 module can be invoked as a script to print a dm4 file’s full directory to the command line. This is helpful when determining the exact structure of a specific DM4 file:

python -m dm4 your_dm4_file.dm4

Helper Functions

Print all of the tags and directories contained in a dm4 file to the console:

dm4.print_tag_directory_tree(dmfile: DM4File, dir_obj: DM4TagDir, indent_level: int = 0)

Print data associated with a specific tag to the console, if it is printable:

dm4.print_tag_data(dmfile: DM4File, tag: Union[DM4TagHeader, DM4DirHeader], indent_level: int)

Todo

Reading arrays of groups has not been implemented.