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User group, tcspc offset and markers #46

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User group, tcspc offset and markers #46

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211a6ed
Implement changes from zoom meeting adding user group and markers
harripd Jul 31, 2024
952c377
Clarification of user and setup/detectors fields
harripd Aug 18, 2024
417ecf6
Fix spelling error
harripd Aug 29, 2024
656ef13
Changed markers to non_photon_ch
harripd Sep 9, 2024
bca70a1
Clarified non-photon IDs and discouraged their use
harripd Oct 29, 2024
e4a3ce0
Defined backwards compatibility
harripd Nov 26, 2024
94b908a
Fix indentation issue
harripd Dec 30, 2024
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4 changes: 2 additions & 2 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,9 +64,9 @@
# built documents.
#
# The short X.Y version.
version = '0.4'
version = '0.5'
# The full version, including alpha/beta/rc tags.
release = '0.4'
release = '0.5'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
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15 changes: 9 additions & 6 deletions docs/generic.rst
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Expand Up @@ -6,6 +6,9 @@ For measurement types which cannot be described by any other
it is possible to use the "generic" type and use the ``/setup``
fields to describe the exact configuration.

The "generic" type is the encouraged type for most experiments
going forward, as it supports arbitrary configurations.


Examples
--------
Expand All @@ -25,8 +28,8 @@ A setup detecting two polarizations in the detection path will be defined by::
and will also specify the detector used for each polarizations::

/photon_data/measurement_specs/detectors_specs/
polarization_ch1 = 0
polarization_ch2 = 1
polarization_ch1 = [0, ]
polarization_ch2 = [1, ]

(where the values 0 and 1 are only examples). In addition ``/setup/lifetime``
will indicate whether the measurement has TCSPC data or not. Finally, the optional field
Expand All @@ -46,8 +49,8 @@ in two using a non-polarizing beam splitter will be defined by::
and the measurement_specs will contain::

/photon_data/measurement_specs/detectors_specs/
split_ch1 = 0
split_ch2 = 1
split_ch1 = [0, ]
split_ch2 = [1, ]

(where the values 0 and 1 are only examples). In addition ``/setup/lifetime``
will indicate whether the measurement has TCSPC data or not. Finally, the optional
Expand All @@ -74,8 +77,8 @@ as in the "smFRET" ``measurement_type``. In particular::
and::

/photon_data/measurement_specs/detectors_specs/
spectral_ch1 = 0
spectral_ch2 = 1
spectral_ch1 = [0, ]
spectral_ch2 = [1, ]

TCSPC measurements
^^^^^^^^^^^^^^^^^^
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2 changes: 1 addition & 1 deletion docs/limitations.rst
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Expand Up @@ -9,7 +9,7 @@ please contact us.
Timestamps with rollover
------------------------

In Photon-HDF5 timestamps are always signed 64 bit integers. Thanks to
In Photon-HDF5 timestamps are usually signed 64 bit integers. Thanks to
compression, there is no size penalty compared to 32 bit integers. Most
timestamping hardware produce a timestamp with 24 or 32 bits
and a rollover flag in order to compute the full "unwrapped" timestamp.
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