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Description:

femtoapiwrap 0.5.4

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 sales@femtonics.eu.

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.