femtoapiwrap 0.5.2

FemtoAPI Python wrapper

Contents

This project contains a Python wrapper for calling the Femto API functions of MESc software and additional utilities for handling the data obtained from the API. These are bundled in the femtoapiwrap package that gets installed using basic setup.

For sample implementations for basic use cases, see the scripts in folder examples/basic.

Modules (it’s enough to import femtoapiwrap only):

• femtoapiwrap.api: the low-level API functions

• femtoapiwrap.hi: high-level types and methods

• femtoapiwrap.utils: miscellaneous functions

• femtoapiwrap.errors: custom exceptions

Install

Basic Setup

$ cd <project-root>
$ pip install -U .

Checking version:

import femtoapiwrap
print(femtoapiwrap.__version__)

Running Examples

Examples require additional dependencies, which can be installed like this:

$ pip install -U .[examples]

Generating Documentation

$ cd <project-root>
$ pip install -U .[doc]
$ cd doc
$ make clean
$ make html

Then you can find the documentation at <project-root>/doc/_build/index.html. Rebuilding often requires the deletion of <project-root>/doc/parts/stubs too.

Running Tests

Run tests with coverage report:

$ cd <project-root>
$ pip install .[test]
$ cd <project-root>/tests
$ coverage run --source femtoapiwrap -m unittest discover && coverage report

Some test cases need an accessible microscope or a running measurement. By default, these are skipped and can be activated by setting 1 to the environment variables FEMTOAPIWRAP_TEST_MICROSCOPE or FEMTOAPIWRAP_TEST_ONLINE respectively.

Purchase

To purchase FemtoAPI please contact [e-mail].

Disclaimer

IN NO EVENT SHALL FEMTONICS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF FEMTONICS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

FEMTONICS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED “AS IS”. FEMTONICS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

Changelog

0.5.2

hi.UnitMeta

New attributes t_step_in_ms, t_length_in_ms, t_length_in_ms_actual, file_handle and fs.

hi.Roi.from_tree

Fixed loading optional fields (e. g. viewport_index).

0.5.1

hi.HighFemtoApi.read_points

Fix: no longer raises EmptyJsonError when there are no points in the file.

hi.Roi.to_px_coords

New parameter closed, with plotting example

0.5.0

hi.Point.from_px_coords

Support for 3D points as well.

hi.Roi

Breaking change: removed attributes viewport_rot and viewport_transl due to expected removal from FemtoAPI JSON object.

New attributes first_z_plane and last_z_plane for planned support of ROIs in zStack measurements (not yet implemented in MESc).

hi.Roi.from_px_coords

Breaking change: replaced parameter viewport with viewport_index.

hi.Roi.to_tree

Breaking change: removed parameters as the corresponding tree fields can be filled from the attributes.

hi.{FileMeta, SessionMeta}.from_tree

Temporary fix to allow converted old MESc files pass the version validation.

0.4.0

errors.*

Breaking changes: Exceptions are no longer inherited from IOError as that was merged with OSError and FemtoApiWrapError subclasses do not strictly related to OS error codes.

PEP-8 compliant and more informative naming:

• ConnectionFailed -> ApiConnectionError

• MicroscopeTimedOut -> MeasurementTimeoutError

• NodeNotFound -> NodeNotFoundError

• NoMetaData -> EmptyJsonError

• InvalidDimension -> DimensionError

• InvalidPointGroup -> PointSeriesKeyError

• UnsupportedVersion -> JsonVersionError

errors.ApiCommandError

New exception to contain error information about FemtoAPI command failures.

errors.ApiLoginError

New exception.

errors.NoMeasurementUnit

Removed, merged with NodeNotFoundError

errors.InvalidMeasurementType

Removed, it was unused.

0.3.1

hi.Roi

Added attribute background based on the previously unprocessed JSON-attribute "role".

hi.Roi.from_px_coords

Added parameter background.

0.3.0

hi.HighFemtoApi.online_frames

Fixed to take into account the actual number of frames received from MESc. Breaking change: The actual start index is now included in the iterator. Introduced the parameter strict to enforce chunks of equal length.

0.2.0.post1

Relaxed dependency version requirements.

0.2.0

Initial public release.