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 git@github.com: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 install
This 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.