deploy: ba75793

Author: chiaratomaiuolo

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 27c76b3c1c517459923e4f0fb00a7617
+tags: 645f666f9bcd5a90fca523b33c5a78b7

.doctrees/analysis.doctree

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+:mod:`hexsample.analysis` --- Analysis facilities
+=================================================
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.analysis

.doctrees/api.doctree

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+.. _api:
+
+API
+===
+
+Top-level indices
+-----------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+List of modules
+---------------
+
+.. toctree::
+   :maxdepth: 2
+
+   analysis
+   clustering
+   digi
+   display
+   fileio
+   fitting
+   hexagon
+   mc
+   modeling
+   pprint
+   readout
+   recon
+   rng
+   roi
+   sensor
+   source
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Utils

.doctrees/clustering.doctree

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+:mod:`hexsample.clustering` --- Clustering facilities
+=====================================================
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.clustering

.doctrees/digi.doctree

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+:mod:`hexsample.digi` --- Digitization facilities
+=================================================
+
+This module contains...
+
+Digi event structure
+--------------------
+
+.. literalinclude:: ../hexsample/digi.py
+   :pyobject: DigiEventRectangular
+   :end-before: __post_init__
+
+
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.digi

.doctrees/display.doctree

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+:mod:`hexsample.display` --- Display facilities
+===============================================
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.display

.doctrees/environment.pickle

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+:mod:`hexsample.fileio` --- Input/Output
+========================================
+
+This module contains all the I/O related facilities, that is, the basic definition
+of the file format and the proper classes to create and read back data files.
+
+.. warning::
+   We have made the provisional decision to have all the I/O implemented in the
+   HDF5 format, which seems to be widely used and to support all the basic
+   features that we need. That said, there seems to be two actively maintained
+   Python interfaces to the HDF5 standard, implemented according to radically ]
+   different design principle, namely:
+
+   * `pytables <https://www.pytables.org/index.html>`_;
+   * `h5py <https://www.h5py.org/>`_.
+
+   It is not trivial for a non expert to really understand which one is more
+   suited to our purposes, and we opted for ``pytables``, but this is a part of
+   the package that might see drastic changes in the future.
+
+
+Base classes
+------------
+
+The module provides base classes for input and output files, than are then
+specialized for, e.g., digitized or reconstructed data.
+
+:class:`OutputFileBase <hexsample.fileio.OutputFileBase>` is the base class for
+output files. Instantiating an object of this class causes the output file to
+be opened in write mode, and a ``header`` node to be created that can be
+used to store arbitrary user attributes---typically to keep track of the
+simulation or reconstruction settings. The file header can bu updated via the
+:meth:`update_header() <hexsample.fileio.OutputFileBase.update_header>` call, which
+loops over the keyword arguments and set the attributes one at a time.
+
+:class:`InputFileBase <hexsample.fileio.InputFileBase>` is the base class for
+input files. Instantiating an object of this class causes the input file to be
+opened in read mode and the header information to be rebuilt in the form of a
+dictionary.
+
+
+Digitized data
+--------------
+
+The basic content of a digitized event contains all the event-by-event data that
+would ordinarily be written out by the DAQ, i.e., the trigger identifier, the
+timestamp, and all the quantities that are necessary in order to uniquely identify
+the region of interest:
+
+.. literalinclude:: ../hexsample/fileio.py
+   :pyobject: DigiDescription
+
+In addition, the PHA content of the ROI (which is a variable-length array by its
+very nature), is encapsulated in a separate ``VLArray`` object in the same
+group holding the digi table.
+
+For simulated data, digitized files contain an additional table encapsulating the
+ground truth information for the event.
+
+.. literalinclude:: ../hexsample/fileio.py
+   :pyobject: MonteCarloDescription
+
+
+Reconstructed data
+------------------
+
+Reconstructed files contain all the reconstruction output, that is: all the quantities
+in the underlying digi file that are relevant for science analysis (i.e., timestamp
+and ROI size), and all the additional quantities that are calculated as part of
+the standard reconstruction (i.e., energy and position).
+
+.. literalinclude:: ../hexsample/fileio.py
+   :pyobject: ReconDescription
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.fileio

.doctrees/fileio.doctree

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+:mod:`hexsample.fitting` --- Advanced fitting
+=============================================
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.fitting

.doctrees/fitting.doctree

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+:mod:`hexsample.hexagon` --- Hexagonal sampling
+===============================================
+
+
+The module is an attempt at having a fully-fledged version of all the necessary
+facilities related to the geometry on an hexagonal grid all in the same place,
+most of the information coming from https://www.redblobgames.com/grids/hexagons/.
+
+
+As a very quick, top level recap, hexagonal grids are classified according
+to their orientation as either pointy-top (with staggered rows, in a vertical layout)
+or flat-top (with staggered columns, in a horizontal layout).
+Each layout comes into versions, depending on whether even or odd rows/columns
+are shoved right/down. We end up with the four basic arrangements shown in the
+figure below, all of which are supported.
+
+.. figure:: figures/hexagonal_layouts.png
+
+The module provides a :class:`HexagonalGrid <hexsample.hexagon.HexagonalGrid>` class,
+representing an hexagonal grid, whose main public interfaces,
+:meth:`pixel_to_world(col, row) <hexsample.hexagon.HexagonalGrid.pixel_to_world>`
+and :meth:`world_to_pixel(x, y) <hexsample.hexagon.HexagonalGrid.world_to_pixel>`,
+allow to go back and forth from logical to physical coordinates and vice versa.
+It is worth pointing out that, in all four cases, the origin of the physical
+reference system is assumed to be at the center of the grid, as illustrated in the
+image.
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.hexagon

.doctrees/hexagon.doctree

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+.. hexsample documentation master file, created by
+   sphinx-quickstart on Sun Sep 24 08:14:51 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+====================================
+hexsample (X-ray hexagonal sampling)
+====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   install
+   api
+   release
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

.doctrees/index.doctree

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+.. _install:
+
+Installation
+============

.doctrees/install.doctree

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+:mod:`hexsample.mc` --- Monte Carlo facilities
+==============================================
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.mc

.doctrees/mc.doctree

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+:mod:`hexsample.modeling` --- Fitting models
+============================================
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.modeling

.doctrees/modeling.doctree

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+:mod:`hexsample.pprint` --- Pretty printing
+===========================================
+
+This module provides facilities for pretty printing, including support for
+colors and special effects in the terminal, and other functions that are useful
+for ASCII-art like rendering. Most notably, this is useful in
+:class:`DigiEvent <hexsample.digi.DigiEvent>`.
+
+.. seealso:: :mod:`hexsample.digi`
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.pprint

.doctrees/pprint.doctree

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+:mod:`hexsample.readout` --- Readout facilities
+===============================================
+
+This module contains...
+
+
+Digitization process
+--------------------
+
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.readout

.doctrees/readout.doctree

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+:mod:`hexsample.recon` --- Event reconstruction
+===============================================
+
+
+Module documentation
+--------------------
+
+.. automodule:: hexsample.recon