dm4

A simple 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 https://personal.ntu.edu.sg/cbb/info/dmformat/index.html. Thank you!

Installation

Install using pip from the command line:

pip install dm4

Example

Create a virtual environment:

python -m venv .venv

Activate the virtual environment:

source .venv/bin/activate

Install the dm4 package along with dependencies for the example:

pip install dm4[example]

Create a Python script, example_dm4.py, with the following content:

import dm4
import numpy as np

from PIL import Image

with dm4.DM4File.open("replace-me.dm4") as dm4data:
   tags = dm4data.read_directory()

   image_data_tag = (
      tags.named_subdirs["ImageList"].unnamed_subdirs[1].named_subdirs["ImageData"]
   )
   image_tag = image_data_tag.named_tags["Data"]

   XDim = dm4data.read_tag_data(
      image_data_tag.named_subdirs["Dimensions"].unnamed_tags[0]
   )
   YDim = dm4data.read_tag_data(
      image_data_tag.named_subdirs["Dimensions"].unnamed_tags[1]
   )

   np_array = np.array(dm4data.read_tag_data(image_tag), dtype=np.uint16)
   np_array = np.reshape(np_array, (YDim, XDim))

   output_fullpath = "example.tif"
   image = Image.fromarray(np_array, "I;16")
   image.save(output_fullpath)

Run the script:

python example_dm4.py

Todo

Reading arrays of groups has not been implemented.