Initial public release

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# PyCharm project settings
+.idea/
+
+# VS Code settings
+.vscode/
+
+# Sublime Text settings
+*.sublime-project
+*.sublime-workspace
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# MacOS junk
+.DS_Store
+*.swp
+
+# LaTeX and Tikz
+*.aux
+*.log
+*.pdf

.readthedocs.yml

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+version: 2
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt

CHANGES.rst

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+Changes
+=======
+
+v0.1.0
+------
+Released June 12, 2020
+
+* Initial public release

LICENSE.rst

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+Copyright (c) 2020, California Institute of Technology ("Caltech"). U.S.
+Government sponsorship acknowledged.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

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+Lentil
+======
+Lentil is a Python library for modeling the imaging chain of an optical system.
+It was originally developed at NASA's Jet Propulsion Lab by the Wavefront Sensing and
+Control group (383E) to provide an easy to use framework for simulating point spread
+functions of segmented aperture telescopes.
+
+Lentil provides classes for representing optical elements with a simple interface for
+including effects like wavefront error, radiometric properties, and various noise and
+aberration sources. Lentil also provides numerical methods for performing Fraunhofer
+(far-field) diffraction calculations. The collection of classes provided by Lentil can
+be used to simulate imagery for a wide variety of optical systems.
+
+Lentil is still under active development and new features continue to be added. Until
+Lentil reaches version 1.0, the API is not guaranteed to be stable, but changes breaking
+backwards compatibility will be noted.
+
+Installing
+----------
+Install and update using `pip`_:
+
+.. code-block:: text
+
+    pip install lentil
+
+Links
+-----
+* Documentation: https://lentil.readthedocs.io/
+* Releases: https://pypi.org/project/lentil/
+* Code: https://github.com/andykee/lentil/
+* Issue tracker: https://github.com/andykee/lentil/issues/
+
+.. _pip: https://pip.pypa.io/en/stable/quickstart/

docs/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)

docs/_img/python/getting_started.py

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+import numpy as np
+import matplotlib.pyplot as plt
+import monocle as mo
+
+pm_mask = mo.util.circle(shape=(512, 512), radius=256)
+sm_obsc = mo.util.circle(shape=(512, 512), radius=256/3)
+sm_obsc_vert = np.zeros((512,512))
+sm_obsc_vert[:, 252:258] = 1
+sm_obsc_horiz = np.zeros((512, 512))
+sm_obsc_horiz[252:258, :] = 1
+mask = pm_mask - sm_obsc - sm_obsc_vert - sm_obsc_horiz
+mask[np.where(mask < 0)] = 0  # Make the mask binary (0's and 1's)
+plt.imshow(mask)
+plt.savefig('../../_static/img/quickstart_pupil.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+simple_pupil = mo.Pupil(diameter=0.5, focal_length=10, pixelscale=0.5/512, amplitude=mask)
+simple_detector = mo.Detector(pixelscale=15e-6, shape=(512, 512))
+planes = [simple_pupil, simple_detector]
+psf = mo.propagate(planes, wave=550e-9, npix=(128,128))
+plt.imshow(psf**0.1)
+plt.savefig('../../_static/img/quickstart_psf_550_native.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+
+psf = mo.propagate(planes, wave=np.arange(450e-9,650e-9,10e-9), npix=(128,128), oversample=5, rebin=False)
+
+plt.imshow(psf**0.1)
+plt.savefig('../../_static/img/quickstart_psf_broadband_5.png', transparent=True, bbox_inches='tight', dpi=150)
+
+
+simple_pupil = mo.Pupil(diameter=0.5,
+                        focal_length=10,
+                        pixelscale=0.5/512,
+                        amplitude=mask,
+                        phase=-1400e-9 * mo.zernike.zernike(mask, index=11))
+plt.imshow(simple_pupil.phase)
+plt.savefig('../../_static/img/quickstart_opd_spherical.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+planes = [simple_pupil, simple_detector]
+psf = mo.propagate(planes, wave=np.arange(475e-9,485e-9,1e-9), npix=(128,128))
+plt.imshow(psf**0.1)
+plt.savefig('../../_static/img/quickstart_psf_480_spherical.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+
+qe = mo.radiometry.Spectrum(wave=[400, 600, 1000], value=[0.4, 0.8, 0.05], waveunit='nm', valueunit=None)
+gain = mo.detector.Gain(gain=0.0016, saturation_capacity=10000)
+simple_detector = mo.FPA(pixelscale=15e-6, shape=(512, 512), qe=qe, gain=gain)
+irrad = np.tile(np.arange(512)/511, (512,1))  # gradient spanning [0, 1]
+flux = irrad * 15000  # flux spanning [0, 15000] e-
+plt.imshow(flux, cmap='gray')
+plt.colorbar()
+plt.savefig('../../_static/img/quickstart_detector_irradiance.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+
+img = simple_detector.frame(flux, ts=1.5, wave=650, waveunit='nm')
+plt.imshow(img, cmap='gray')
+plt.colorbar()
+plt.savefig('../../_static/img/quickstart_detector_frame.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+
+detector_attrs = {
+        'qe': qe,
+        'gain': mo.detector.Gain(gain=2**12/15000, saturation_capacity=15000),
+        'shot_noise': mo.detector.ShotNoise(),
+        'read_noise': mo.detector.ReadNoise(50),
+        'dark_signal': mo.detector.DarkCurrent(500)}
+
+simple_detector = mo.FPA(pixelscale=15e-6, shape=(512, 512), **detector_attrs)
+simple_pupil = mo.Pupil(diameter=0.5,
+                        focal_length=10,
+                        pixelscale=0.5/512,
+                        amplitude=mo.util.normalize_power(mask),
+                        phase=-1400e-9 * mo.zernike.zernike(mask, index=11))
+
+src = mo.radiometry.Blackbody.vegamag(wave=np.arange(350, 750),
+                                      temp=9500,
+                                      mag=8,
+                                      band='V')
+
+ir_filter = mo.radiometry.Spectrum(wave=[350, 395, 400, 700, 705, 750], value=[0, 0, 0.8, 0.8, 0, 0])
+collecting_area = np.pi*(simple_pupil.diameter/2 - simple_pupil.diameter/6)**2
+irradiance = src * ir_filter * collecting_area
+
+fig, ax = plt.subplots(3,1, figsize=[5, 5])
+
+ax[0].plot(src.wave, src.value)
+ax[0].grid()
+ax[0].set_ylim([40000,80000])
+ax[0].set_title('Stellar flux')
+ax[0].set_ylabel('ph/s/m^2/λ')
+
+ax[1].plot(ir_filter.wave, ir_filter.value)
+ax[1].grid()
+ax[1].set_ylim([0,1])
+ax[1].set_title('IR filter')
+ax[1].set_ylabel('a.u.')
+
+ax[2].plot(irradiance.wave, irradiance.value)
+ax[2].grid()
+ax[2].set_ylim([0,6000])
+ax[2].set_title('Detector irradiance')
+ax[2].set_ylabel('ph/s/λ')
+ax[2].set_xlabel('Wavelength [nm]')
+
+plt.tight_layout()
+plt.savefig('../../_static/img/quickstart_source.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()
+
+
+wave = np.arange(350,750,10)
+binned_irradiance = irradiance.bin(wave)
+planes = [simple_pupil, simple_detector]
+psf = mo.propagate(planes, wave=wave*1e-9, weight=binned_irradiance,
+                   npix=(128, 128), flatten=False)
+img = simple_detector.frame(psf, ts=1e-4, wave=wave, collect_charge=True)
+plt.imshow(img, cmap='gray')
+plt.savefig('../../_static/img/quickstart_img.png', transparent=True, bbox_inches='tight', dpi=150)
+plt.close()