From 3312092b94595ee98fa9f39c8bc8bcf48c67e314 Mon Sep 17 00:00:00 2001 From: Antonino Ingargiola Date: Thu, 26 Feb 2015 15:26:51 -0800 Subject: [PATCH] Update overview section --- docs/index.rst | 6 +++--- docs/phdata.rst | 25 ++++++++++++++++++------- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 20df364..2bcea2c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -8,13 +8,13 @@ Photon-HDF5 file format documentation :Authors: Antonino Ingargiola, Xavier Michalet, Ted Laurence :Contact: tritemio@gmail.com -:Version: 0.2 +:Version: 0.3 .. note :: - This document describes the version "0.2-Draft" of the + This document describes the version "0.3" of the **Photon-HDF5 file format**. The latest version of this document can be found at - `http://photon-hdf5.readthedocs.org `__. + `http://photon-hdf5.readthedocs.org `__. Photon-HDF5 is a file format for a class of single-molecule spectroscopy experiments that requires storing photon stream data. diff --git a/docs/phdata.rst b/docs/phdata.rst index d9a0b4b..cd1c107 100644 --- a/docs/phdata.rst +++ b/docs/phdata.rst @@ -11,15 +11,25 @@ An overview of the data format is shown in the following figure: A Photon-HDF5 is a standard HDF5 file with a predefined structure. -Every Photon-HDF5 needs to have a ``photon_data`` group that +Every Photon-HDF5 file has a ``photon_data`` group that contains the photon timestamps and other per-photon data. +In the most basic form ``photon_data`` contains only the per-photon data +(timestamps, detectors, nanotimes, etc...). However, in order to correctly +interpret the data, additional information is needed (for example +which detector is donor/acceptor in a 2-colors smFRET experiment, or the +alternation period in a us-ALEX experiment). These additional specifications, +if present, are contained inside **/photon_data** in the +**measuremet_specs** sub-group. -Other optional groups: +Other optional groups are: -- ``indentity`` -- ``provenance`` -- ``setup`` -- ``sample`` +- **/indentity**: information about the data file +- **/provenance**: information about the original data file +- **/setup**: fundamental parameters of the experimental setup +- **/sample**: sample information. + +The following sections describe in details all the Photon-HDF5 +groups and fields. Root-level parameters --------------------- @@ -44,7 +54,8 @@ Optional if there is only 1 detector: - **detectors** -Optional: +In addition, when the dataset contain nanotime information, the following +fields must be present: - **nanotimes** - **nanotimes_specs/**