A library for loading various Atomic Force Microscopy (AFM) file formats into Python. This library is primarily intended for use with TopoStats.
Supported file formats
| File format | Description |
|---|---|
.asd |
High-speed AFM |
.ibw |
WaveMetrics |
.spm |
Bruker's Format |
.jpk |
Bruker |
.topostats |
TopoStats |
.gwy |
[Gwydion] (http://gwyddion.net) |
Support for the following additional formats is planned. Some of these are already supported in TopoStats and are awaiting refactoring to move their functionality into AFMReader these are denoted in bold below.
| File format | Description | Status |
|---|---|---|
.nhf |
Nanosurf | To Be Implemented. |
.aris |
Imaris Oxford Instruments | To Be Implemented. |
.tiff |
Park Systems | To Be Implemented. |
If you wish to process AFM images supported by AFMReader it is recommend you use
TopoStats to do so, however the library can be used on its own.
You can open .topostats files using the load_topostats function. Just pass in the path to the file.
from AFMReader.topostats import load_topostats
image, pixel_to_nanometre_scaling_factor, metadata = load_topostats(file_path="./my_topostats_file.topostats")You can open .spm files using the load_spm function. Just pass in the path to the file and the
channel name that you want to use. (If in doubt use one of the following: "Height", "ZSensor",
"Height Sensor").
from AFMReader.spm import load_spm
image, pixel_to_nanometre_scaling_factor = load_spm(file_path="./my_spm_file.spm", channel="Height")You can open .gwy files using the load_gwy function. Just pass in the path to the file and the
channel name that you want to use. (If in doubt use one one of the following: "Height", "ZSensor",
"Height Sensor").
from AFMReader.gwy import load_gwy
image, pixel_to_nanometre_scaling_factor = load_gwy(file_path="./my_gwy_file.gwy", channel="Height")You can open .asd files using the load_asd function. Just pass in the path to the file and the channel name that you
want to use. (If in doubt use the "TP" topography channel).
Note: For .asd files, there seem to only ever be two channels in one file. "TP" (topography) is the main one you
will want to use unless you know you specifically want something else.
Other channels: "ER" - Error, "PH" - Phase
from AFMReader.asd import load_asd
frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd", channel="TP")You can open .ibw files using the load_ibw function. Just pass in the path to the file
and the channel name that you want to use. (If in doubt, use HeightTracee (yes, with the
extra 'e'), ZSensorTrace, or ZSensor).
from AFMReader.ibw import load_ibw
image, pixel_to_nanometre_scaling_factor = load_ibw(file_path="./my_ibw_file.ibw", channel="HeightTracee")You can open .jpk files using the load_jpk function. Just pass in the path
to the file and the channel name you want to use. (If in doubt, use height_trace or measuredHeight_trace).
from AFMReader.jpk import load_jpk
image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk", channel="height_trace")Bug reports and feature requests are welcome. Please search for existing issues, if none relating to your bug/feature are found then feel free to create a new issue detailing what went wrong or the feature you would like to see implemented.
Pull requests are also welcome, please note that we have a Code of Conduct.
We use pre-commit to apply linting via ruff and
pylint pre-commit hooks and use the
Black and Flake8 code styles. To set yourself up for
contributing after cloning the package and creating a Python virtual environment you should install the development
dependencies and pre-commit as shown below.
# Activate your virtual environment, this will depend on which system you use e.g. conda or virtualenvwrapper
# Clone the repository
git clone [email protected]:AFM-SPM/AFMReader.git
# Change directories into the newly cloned directory
cd AFMReader
# Install the package along with the optional development (dev) dependencies
pip install -e .[dev]
# Install pre-commit
pre-commit installThis will ensure that any commits and pull requests you make will pass the Pre-commit Continuous
Integration. Where possible ruff will correct the changes it can, but it may require you to
address some issues manually, before adding any changes and attempting to commit again.
![pre-commit-ci[bot] avatar](https://avatars.githubusercontent.com/in/68672?v=4 "pre-commit-ci[bot]")
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