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drombas committed Feb 26, 2024
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4 changes: 4 additions & 0 deletions .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: 7a31681a7c78008b4e2dccbaa2239b97
tags: 645f666f9bcd5a90fca523b33c5a78b7
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138 changes: 138 additions & 0 deletions _sources/functions.rst.txt
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=========
Functions
=========

These are all the functions implemented in RETIMAT


File reading
============

.. autofunction:: io.read_vol

----

.. autofunction:: io.read_e2e

----

.. autofunction:: io.read_img

----

.. autofunction:: io.read_bin

----

.. autofunction:: io.read_fda

----

.. autofunction:: io.read_xml_iowa

----


Visualization
=============

.. autofunction:: visu.generate_report

----

.. autofunction:: visu.plot_sectors

----

.. autofunction:: visu.spider_plot

----


Reflectance
===========

.. autofunction:: reflectance.compute_attenuation

----

.. autofunction:: reflectance.image_quality

----

.. autofunction:: reflectance.normalize_reflectance

----

.. autofunction:: reflectance.reflectance_map

----

.. autofunction:: reflectance.stack_bscans

----

Structural analysis
===================

.. autofunction:: structure.compute_thickness

----

.. autofunction:: structure.fit_pit_model

----

.. autofunction:: structure.get_morph_params

----

.. autofunction:: structure.smooth_pit

----

Spatial analysis
================

.. autofunction:: spatial.find_fovea

----

.. autofunction:: spatial.flip_coordinates

----

.. autofunction:: spatial.get_ascan_coordinates

----

.. autofunction:: spatial.resample_map

----

.. autofunction:: spatial.sectorize_map

----

.. autofunction:: spatial.sectorize_peripapillar

----

Texture analysis
================

.. autofunction:: texture.fractal_dimension

----

.. autofunction:: texture.GLCM_features

----

.. autofunction:: texture.lacunarity

----

.. autofunction:: texture.LBP_features


44 changes: 44 additions & 0 deletions _sources/index.rst.txt
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.. RETIMAT documentation master file, created by
sphinx-quickstart on Mon Apr 10 19:51:04 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Home
====

RETIMAT is MATLAB toolbox for retinal OCT image analysis.

.. image:: https://user-images.githubusercontent.com/50577357/198825276-a70c2cc9-6fd4-408c-8adb-d9f7fcd8d6de.png
:width: 1000
:alt: Alternative text

What can I do with RETIMAT
^^^^^^^^^^^^^^^^^^^^^^^^^^

* Read OCT files: ``vol``, ``e2e``, ``fda``, ``img``, ``OCTExplorer``
* Visualize images
* Feature extraction: thickness, foveal pit morphology, texture

How to install it
^^^^^^^^^^^^^^^^^

1. Download the code from `here <https://zenodo.org/record/7313091#.ZDVXQLxBz1s>`_
2. Unzip the downloaded file
3. Execute the ``startup.m`` script from the main folder
4. Follow the tutorials or reach out for help

How to use it
^^^^^^^^^^^^^
.. toctree::
:hidden:

self
.. toctree::
:maxdepth: 2

tutorials
functions

Contact
^^^^^^^
For help, feedback or collaboration inquiries please contact dromero.research@gmail.com
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