# Xarray plugin to read Nanonis spectroscopy .dat files
[](https://pypi.org/project/nanonis-xarray/)
[](https://anaconda.org/conda-forge/nanonis-xarray)
[](https://pypistats.org/packages/nanonis-xarray)
[](https://github.com/angelo-peronio/nanonis-xarray/blob/master/LICENSE)
[](https://pypi.org/project/nanonis-xarray/)
[](https://github.com/angelo-peronio/nanonis-xarray/actions/workflows/ci.yaml)
[](https://results.pre-commit.ci/latest/github/angelo-peronio/nanonis-xarray/master)
[](https://codecov.io/github/angelo-peronio/nanonis-xarray)
[](https://scientific-python.org/specs/spec-0000/)
[](https://github.com/astral-sh/ruff)
[](https://doi.org/10.5281/zenodo.17095214)
`nanonis-xarray` is a [`xarray`](https://xarray.dev/) plugin to read spectroscopy measurements saved in text
format (`.dat`) by a [Nanonis Mimea](https://www.specs-group.com/nanonis/products/mimea/)
SPM control system from [SPECS Surface Nano Analysis GmbH](https://www.specs-group.com/).
The data is read into a [`xarray.Dataset`](https://docs.xarray.dev/en/stable/getting-started-guide/why-xarray.html#core-data-structures), where each measured channel (tunnelling current, AFM oscillation amplitude, …) is a [`xarray.DataArray`](https://docs.xarray.dev/en/stable/user-guide/data-structures.html#dataarray) with up to three dimensions:
* The independent variable of the measurement, such as sample bias voltage or tip z position;
* The sweep number, if the measurement has been repeated multiple times;
* The sweep direction (forward or backward), if the independent variable has been swept in both directions.
```python
>>> import xarray as xr
>>> data = xr.open_dataset("tests/data/z.dat")
>>> data.coords
Coordinates:
* z_rel (z_rel) float64 2kB [m] -2.1e-10 -2.065e-10 ... 4.865e-10 4.9e-10
* sweep (sweep) int64 24B 1 2 3
* direction (direction) object 16B 'bw' 'fw'
```
[`pint-xarray`](https://xarray.dev/blog/introducing-pint-xarray) is used to associate a physical unit to each channel, unless `xr.open_dataset()` is called with `quantify_vars=False`:
```python
>>> data["current"].pint.units
<Unit('ampere')>
```
The header of the measurement is stored in the `attrs` nested dictionary:
```python
>>> data.attrs["Z Spectroscopy"]["Number of sweeps"]
3
>>> data.attrs["Z Spectroscopy"]["backward sweep"]
True
```
Physical quantities are stored as [`pint.Quantity`](https://pint.readthedocs.io/en/stable/getting/tutorial.html#defining-a-quantity), timestamps as [`datetime.datetime`](https://docs.python.org/3/library/datetime.html#datetime-objects), and paths as [`pathlib.Path`](https://docs.python.org/3/library/pathlib.html#basic-use):
```python
>>> data.attrs["NanonisMain"]["RT Frequency"]
<Quantity(10000.0, 'hertz')>
>>> data.attrs["Date"]
datetime.datetime(2015, 3, 27, 11, 49, 5)
```
## 🚧 Work in progress 🚧
This library is under development: expect breaking changes. Nanonis binary formats (`.sxm`, `.3ds`) are currently not supported, and can be read by similar projects:
* [`nanonispy2`](https://github.com/ceds92/nanonispy2)
* [`xarray-nanonis`](https://github.com/John3859/xarray-nanonis)
* ... and [many more](https://pypi.org/search/?q=nanonis).
## How to cite
Cite `nanonis-xarray` in your published work using the metadata in [`CITATION.cff`](CITATION.cff).
Specific DOIs and BibTeX entries for each released version can be found on [Zenodo](https://doi.org/10.5281/zenodo.17095214).
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"description": "# Xarray plugin to read Nanonis spectroscopy .dat files\n\n[](https://pypi.org/project/nanonis-xarray/)\n[](https://anaconda.org/conda-forge/nanonis-xarray)\n[](https://pypistats.org/packages/nanonis-xarray)\n[](https://github.com/angelo-peronio/nanonis-xarray/blob/master/LICENSE)\n[](https://pypi.org/project/nanonis-xarray/)\n[](https://github.com/angelo-peronio/nanonis-xarray/actions/workflows/ci.yaml)\n[](https://results.pre-commit.ci/latest/github/angelo-peronio/nanonis-xarray/master)\n[](https://codecov.io/github/angelo-peronio/nanonis-xarray)\n[](https://scientific-python.org/specs/spec-0000/)\n[](https://github.com/astral-sh/ruff)\n[](https://doi.org/10.5281/zenodo.17095214)\n\n`nanonis-xarray` is a [`xarray`](https://xarray.dev/) plugin to read spectroscopy measurements saved in text\nformat (`.dat`) by a [Nanonis Mimea](https://www.specs-group.com/nanonis/products/mimea/)\nSPM control system from [SPECS Surface Nano Analysis GmbH](https://www.specs-group.com/).\n\nThe data is read into a [`xarray.Dataset`](https://docs.xarray.dev/en/stable/getting-started-guide/why-xarray.html#core-data-structures), where each measured channel (tunnelling current, AFM oscillation amplitude, \u2026) is a [`xarray.DataArray`](https://docs.xarray.dev/en/stable/user-guide/data-structures.html#dataarray) with up to three dimensions:\n\n* The independent variable of the measurement, such as sample bias voltage or tip z position;\n* The sweep number, if the measurement has been repeated multiple times;\n* The sweep direction (forward or backward), if the independent variable has been swept in both directions.\n\n```python\n>>> import xarray as xr\n\n>>> data = xr.open_dataset(\"tests/data/z.dat\")\n>>> data.coords\nCoordinates:\n * z_rel (z_rel) float64 2kB [m] -2.1e-10 -2.065e-10 ... 4.865e-10 4.9e-10\n * sweep (sweep) int64 24B 1 2 3\n * direction (direction) object 16B 'bw' 'fw'\n\n```\n\n[`pint-xarray`](https://xarray.dev/blog/introducing-pint-xarray) is used to associate a physical unit to each channel, unless `xr.open_dataset()` is called with `quantify_vars=False`:\n\n```python\n>>> data[\"current\"].pint.units\n<Unit('ampere')>\n\n```\n\nThe header of the measurement is stored in the `attrs` nested dictionary:\n\n```python\n>>> data.attrs[\"Z Spectroscopy\"][\"Number of sweeps\"]\n3\n>>> data.attrs[\"Z Spectroscopy\"][\"backward sweep\"]\nTrue\n\n```\n\nPhysical quantities are stored as [`pint.Quantity`](https://pint.readthedocs.io/en/stable/getting/tutorial.html#defining-a-quantity), timestamps as [`datetime.datetime`](https://docs.python.org/3/library/datetime.html#datetime-objects), and paths as [`pathlib.Path`](https://docs.python.org/3/library/pathlib.html#basic-use):\n\n```python\n>>> data.attrs[\"NanonisMain\"][\"RT Frequency\"]\n<Quantity(10000.0, 'hertz')>\n>>> data.attrs[\"Date\"]\ndatetime.datetime(2015, 3, 27, 11, 49, 5)\n\n```\n\n## \ud83d\udea7 Work in progress \ud83d\udea7\n\nThis library is under development: expect breaking changes. Nanonis binary formats (`.sxm`, `.3ds`) are currently not supported, and can be read by similar projects:\n\n* [`nanonispy2`](https://github.com/ceds92/nanonispy2)\n* [`xarray-nanonis`](https://github.com/John3859/xarray-nanonis)\n* ... and [many more](https://pypi.org/search/?q=nanonis).\n\n## How to cite\n\nCite `nanonis-xarray` in your published work using the metadata in [`CITATION.cff`](CITATION.cff).\nSpecific DOIs and BibTeX entries for each released version can be found on [Zenodo](https://doi.org/10.5281/zenodo.17095214).\n",
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