Expanded File support

What's Changed

PQ: Workaround decoding error for non-UTF-8 strings by @tritemio in https://github.com/Photon-HDF5/phconvert/pull/36
Add support for PHU and for duplicated tags in PTU by @tritemio in https://github.com/Photon-HDF5/phconvert/pull/37
Update pqreader.py by @seb5g in https://github.com/Photon-HDF5/phconvert/pull/34
Appveyor: activate base env before using conda build. by @tritemio in https://github.com/Photon-HDF5/phconvert/pull/42
Add tests for PHU files by @tritemio in https://github.com/Photon-HDF5/phconvert/pull/43
bhprintsys_params: update to python3 and other enhancements. by @dmopalmer in https://github.com/Photon-HDF5/phconvert/pull/46
Ensure h5file is closed even if validation fails by @ramenbytes in https://github.com/Photon-HDF5/phconvert/pull/52
Avoid copying data array when loading sm files by @ramenbytes in https://github.com/Photon-HDF5/phconvert/pull/49
Combined updates by @harripd in https://github.com/Photon-HDF5/phconvert/pull/57
Updates for 0.9.1 by @harripd in https://github.com/Photon-HDF5/phconvert/pull/58

New Contributors

@seb5g made their first contribution in https://github.com/Photon-HDF5/phconvert/pull/34
@dmopalmer made their first contribution in https://github.com/Photon-HDF5/phconvert/pull/46
@ramenbytes made their first contribution in https://github.com/Photon-HDF5/phconvert/pull/52
@harripd made their first contribution in https://github.com/Photon-HDF5/phconvert/pull/57

Full Changelog: https://github.com/Photon-HDF5/phconvert/compare/0.9...0.9.1

- Python
Published by harripd about 2 years ago

phconvert - Version 0.9

Important: This version drops support for Python 2.7. Python 2.7 is approaching end of life and we have no resources to keep supporting it. If you need to run Python 2.7, you can keep using phconvert 0.8.2 or you can pay a developer to support it.

This version improves supports for loading PicoQuant files:

Added support for decoding rtHydraHarpT3 PTU files
Improvements in metadata decoding of HT3 and PT3 files
Loading of ns-ALEX measurement from PTU, HT3 or PT3 files now can be done with a single function (phc.loader.nsalex_pq)

Release sponsored by Prof. Eitan Lerner

- Python
Published by tritemio over 7 years ago

phconvert - Version 0.8.2

Minor release:

Fix a packaging issue for PIP users that caused an error on import due to missing metadata file.

- Python
Published by tritemio over 8 years ago

phconvert - Version 0.8.1

Minor release with improved file validation.

More stringent validation checks (commit https://github.com/Photon-HDF5/phconvert/commit/d463b42574090cb59aef31898f447f63a92feec1)
Add subpackage phconvert.v04 to load and validate Photon-HDF5 v0.4
Fix validation with strict_description = False. Before this change
descriptions checks were not disabled completely when using strict_description = False.
Check that arrays in /photon_data are strictly 1D (commit https://github.com/Photon-HDF5/phconvert/commit/2dde57b216b1d838475e925ee9e904129e3e0f82).

- Python
Published by tritemio over 8 years ago

What's New?

This is a major release of phconvert that adds support for Photon-HDF5 v0.5 and for more input file formats (Picoquant PT3. and .T3R). Many thanks to @biswajitSM for contributing the PT3/T3R feature.

To install or update phconvert use:

conda install phconvert -c conda-forge

NOTE: You can also install phconvert from PyPI.

Note that phconvert 0.8+ will save only Photon-HDF5 v0.5. If you need to save the old Photon-HDF5 v0.4 format, you can use phconvert 0.7.x. The 0.7 branch will receive only critical bug fixes.

Photon-HDF5 version 0.5: This release of phconvert will read an save the new Photon-HDF5 version 0.5. Note that Photon-HDF5 v0.5 is still in "release candidate" stage (rc1). Minor modifications to the format are still possible (but at this point unlikely) before the final 0.5 specs release. You can read in the docs what changed in Photon-HDF5 v0.5. Note that despite being "release candidate", the new Photon-HDF5 v0.5 has already been used to publish data of at least 3 publications in 2017.
PicoQuant PT3 T3R files: We added support for reading T3R files and improved PT3 support. New example notebooks show how to convert ns-ALEX/PIE files saved in PT3 or T3R files to Photon-HDF5.
MyBinder: after a period of breakage due to migration to a new infrastructure, MyBinder works again. You can try converting files online without any installation by clicking here:

- Python
Published by tritemio over 8 years ago

What's New?

Add support for PicoQuant PTU files (for the following t3records formats: rtPicoHarpT3, rtHydraHarp2T3, rtTimeHarp260NT3, rtTimeHarp260PT3)
Add unit test for pqreader.py module
Run bhreader's and pqreader's unit tests on CI services (AppVeyor and TravisCI)

- Python
Published by tritemio over 9 years ago

What's New?

Fix an error when using require_setup=False and the setup group is missing in the input data. See 3514a021830a40ee0d2c4db6b7c90e28224f527f.

- Python
Published by tritemio almost 10 years ago

What's new?

Add support for reading Becker & Hickl SPC from SPC-134/144/154/830
Documentation fixes
From now on conda packages will be built and hosted by conda-forge. As a results you can install phconvert with conda install phconvert -c conda-forge.

Many thanks to @lampo808 for adding the SPC support!

- Python
Published by tritemio almost 10 years ago

What's New?

File decoding

Improved reader for Becker & Hickl SPC files, now more metadata is automatically retrieved.
Add support for decoding PicoQuant PT3 files

Testing

Add support for Continuous Integration. phconvert notebooks are now automatically executed on each commit on windows (AppVeyor) and linux (Travis CI) on python 2.7, 3.4 and 3.5.

Docs

Improved reference documentation now including bhreader docs (read Becker & Hickl files) and an improved pqreader docs (read PicoQuant files).

- Python
Published by tritemio about 10 years ago

phconvert - Version 0.6.9 - The Christmas Release!

What's new?

Fix a runtime error when saving Photon-HDF5 files under python 2 (issue #9 and PR #10).
Fix error message when input file HT3 was not found (bb03cf31d6e552f9abcd004e440f7bb068de3278)
Notebook updates

- Python
Published by tritemio over 10 years ago

What's new?

Small fixes and improvements: - Add option to allow missing setup group (both saving and validation) b35e6d0e7512b8499fb5057da4e279bd68b8afa2 - Better handle input for array fields (e.g. detectors_specs) in a variety of formats (tuple, list, array with ndim=0, array with ndim=1): 1ad5ca93f372cbeb78c9945b7b8234439edb543a and e07ddbac4c80e14da41820039d200cea9614cd1b. - Runtime error fix: d7fff767e019920dc04ed8139468e979b6fc92f8 - Documentation improvements

- Python
Published by tritemio over 10 years ago

phconvert - Version 0.6.7

What's new?

tcspc_range in nanotimes_specs is now optional
matplotlib is now only an optional dependency
More validity tests on Photon-HDF5 files
More input normalization (for YAML) for data_dict argument in save_photon_hdf5()
Tests validity of input data_dict
Update versioneer

- Python
Published by tritemio over 10 years ago

phconvert - Version 0.6.6

What's new?

Fix always-True assertion when loading SPC files

- Python
Published by tritemio over 10 years ago

phconvert - Version 0.6.5

What's new?

Documentation improvement and new API docs: http://phconvert.readthedocs.org/
Add notebook to write Photon-HDF5 files from scratch: Writing Photon-HDF5 files
save_photon_hdf5() improvements:
- Restore input dict sanitization (it was mistakenly disabled)
- Cast bools to ints for improved compatibility
- Auto-compute acquisition_duration for single-spot data
- When not provided, create and populate identity group
- Improve Photon-HDF5 validity test (852242c05864f8cc5a064b00b1c7efac26dfb581)

- Python
Published by tritemio over 10 years ago

phconvert - Version 0.6.4

What's new?

Fix a bug causing file validation to fail (fd0a278679e6d33ee15c9acc5ff194c03e6f36b0)

- Python
Published by tritemio almost 11 years ago

phconvert - Version 0.6.3

What's new?

Rewrite of validation function: now they validates a HDF5 file, not an in-memory representation. This makes easier to test if a file is Photon-HDF5 compliant, regardless if it has been created by phconvert or not.
Added more tests during validation
Fixed error that caused authors and other identity fields not being saved

Previous changes (from version 0.6): - Fix donor/acceptor assignment in conversion notebooks - Fix a string encoding issue (4a95505b5de868cc3ead4258b52f7362f1363732) - Simplify saving custom metadata

- Python
Published by tritemio almost 11 years ago

phconvert - Version 0.6

What's new?

A few important changes: - Automatically convert input of "scalar" fields to scalar if they are arrays or sequences of length == 1. See #5. - Check conformance with the specs in save_photon_hdf5() removing the need to call assert_valid_photon_hdf5() separately. - Remove time_reversed field in nanotimes_specs. Now we use the simpler convention that nanotimes has a time axis direction correctly oriented. See #6.