rename doc folder

doc/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/Tutorial_advanced.rst

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+Tutorial - Advanced (only script)
+=================================
+
+
+
+
+Single acquisition
+------------------
+
+
+This tutorial walks you through the process of running a simple acquisition using the `CassiSystem` class from the :code:`simca` package.
+
+Setup
+.....
+
+First, make sure to import the necessary modules:
+
+.. code-block:: python
+
+   from simca import CassiSystem, load_yaml_config
+
+Next, load the configuration files:
+
+.. code-block:: python
+
+   config_dataset = load_yaml_config("simca/configs/dataset.yml")
+   config_system = load_yaml_config("simca/configs/cassi_system.yml")
+   config_patterns = load_yaml_config("simca/configs/pattern.yml")
+   config_acquisition = load_yaml_config("simca/configs/acquisition.yml")
+
+Then, set the name of the dataset of interest:
+
+.. code-block:: python
+
+   dataset_name = "indian_pines"
+
+Initialize the CassiSystem
+..............................
+
+Initialize the `CassiSystem`:
+
+.. code-block:: python
+
+   cassi_system = CassiSystem(system_config=config_system)
+
+Load the Hyperspectral dataset
+..............................
+
+Load the hyperspectral dataset:
+
+.. code-block:: python
+
+   cassi_system.load_dataset(dataset_name, config_dataset["datasets directory"])
+
+Generate the Coded Aperture Pattern
+........................................
+
+Generate the coded aperture pattern:
+
+.. code-block:: python
+
+   cassi_system.generate_2D_pattern(config_patterns)
+
+Propagate the Coded Aperture Grid
+...................................
+
+Propagate the coded aperture grid to the detector plane:
+
+.. code-block:: python
+
+   cassi_system.propagate_coded_aperture_grid()
+
+Generate the Filtering Cube
+..............................
+
+Generate the filtering cube:
+
+.. code-block:: python
+
+   cassi_system.generate_filtering_cube()
+
+(Optional) Generate the PSF
+..............................
+
+Generate the PSF of the optical system:
+
+.. code-block:: python
+
+   cassi_system.optical_model.generate_psf(type="Gaussian",radius=100)
+
+Simulate the Acquisition
+.........................
+
+Simulate the acquisition (with PSF in this case):
+
+.. code-block:: python
+
+   cassi_system.image_acquisition(use_psf=True, chunck_size=50)
+
+Save the Acquisition
+.........................
+
+Finally, save the acquisition:
+
+.. code-block:: python
+
+   cassi_system.save_acquisition(config_patterns, config_acquisition)
+
+And that's it! You've successfully run an acquisition using the `CassiSystem` class from the :code:`simca` package.
+
+
+Multiple acquisitions
+----------------------
+
+This tutorial walks you through the process of running multiple acquisitions using the `CassiSystem` class from the :code:`simca` package.
+
+Setup
+.........................
+
+First, make sure to import the necessary modules and configurations:
+
+
+.. code-block:: python
+
+   import matplotlib.pyplot as plt
+   from simca import CassiSystem
+   from simca.functions_general_purpose import *
+   import os
+
+   config_dataset = load_yaml_config("simca/configs/dataset.yml")
+   config_system = load_yaml_config("simca/configs/cassi_system.yml")
+   config_patterns = load_yaml_config("simca/configs/pattern.yml")
+   config_acquisition = load_yaml_config("simca/configs/acquisition.yml")
+
+   dataset_name = "indian_pines"
+   results_directory = "./data/results/lego_test_1"
+   nb_of_acq = 10
+
+
+Initialize the CassiSystem
+..................................................
+
+Initialize the `CassiSystem`:
+
+
+.. code-block:: python
+
+   cassi_system = CassiSystem(system_config=config_system)
+
+
+Load the Hyperspectral dataset
+..................................................
+
+Load the hyperspectral dataset:
+
+
+.. code-block:: python
+
+   cassi_system.load_dataset(dataset_name, config_dataset["datasets directory"])
+
+
+Generate Multiple Patterns for Acquisition
+...........................................................................
+
+Generate multiple coded aperture patterns:
+
+
+.. code-block:: python
+
+   cassi_system.generate_multiple_patterns(config_patterns, nb_of_acq)
+
+
+Propagate the Coded Aperture Grid
+..................................................
+
+Propagate the coded aperture grid to the detector plane:
+
+
+.. code-block:: python
+
+   cassi_system.propagate_coded_aperture_grid()
+
+
+Generate Multiple Filtering Cubes
+..................................................
+
+Generate the multiple filtering cubes:
+
+
+.. code-block:: python
+
+   cassi_system.generate_multiple_filtering_cubes(nb_of_acq)
+
+
+Simulate Multiple Acquisitions
+..................................................
+
+Simulate multiple acquisitions:
+
+
+.. code-block:: python
+
+   cassi_system.multiple_image_acquisitions(use_psf=False, nb_of_filtering_cubes=nb_of_acq, chunck_size=50)
+
+
+Save the Acquisition
+.........................
+
+Set up the results directory and save the acquisition:
+
+
+.. code-block:: python
+
+   cassi_system.result_directory = results_directory
+   os.makedirs(results_directory, exist_ok=True)
+   
+   save_config_file("config_system", cassi_system.system_config, cassi_system.result_directory)
+   save_config_file("config_pattern", config_patterns, cassi_system.result_directory)
+   save_config_file("config_acquisition", config_acquisition, cassi_system.result_directory)
+   save_data_in_hdf5("interpolated_scene", cassi_system.interpolated_scene, cassi_system.result_directory)
+   save_data_in_hdf5("panchro", cassi_system.panchro, cassi_system.result_directory)
+   save_data_in_hdf5("wavelengths", cassi_system.optical_model.system_wavelengths, cassi_system.result_directory)
+   save_data_in_hdf5("list_of_compressed_measurements", cassi_system.list_of_measurements, cassi_system.result_directory)
+   save_data_in_hdf5("list_of_filtering_cubes", cassi_system.list_of_filtering_cubes, cassi_system.result_directory)
+   save_data_in_hdf5("list_of_patterns", cassi_system.list_of_patterns, cassi_system.result_directory)
+
+Congratulations! You've successfully performed and saved multiple acquisitions using the `CassiSystem` class from the :code:`simca` package.
+