Merge pull request #15 from JarronL/py3_060

Python 3; WebbPSF 0.6.0

HISTORY.rst

@@ -0,0 +1,41 @@
+Revision History
+================
+
+v0.6.0 (Oct 2017)
+-----------------
+
+- Support for Python 3
+- Updated code comments for ``sphinx`` and ``readthedocs`` documentation
+- Create ``setup.py`` install file
+- Modify grism PSF shapes due to aperture shape
+- Detector frames times based on ASIC microcode build 10
+- Headers for DMS data
+
+v0.5.0 (Feb 2017)
+-----------------
+
+- Initial GitHub release
+- Match version numbering to ``WebbPSF`` equivalent
+- ND Acquisition mode
+- Ramp settings optimizer
+- Can now simulate ramps with detector noise
+- Query Euclid's IPAC server for position-dependent Zodiacal emission
+- Added example Jupyter notebooks
+
+v0.1.2 (Jan 2017)
+-----------------
+- Observations subclass for coronagraphs and direct imaging
+
+v0.1.1 (Sep 2016)
+-----------------
+- Add support for LW slitless grism
+- Add support for extended sources
+
+v0.1.0 (Aug 2016)
+-----------------
+- Rewrite of ``SimNRC`` and rename ``pynrc``
+- Object oriented ``multiaccum``, ``DetectorOps``, and ``NIRCam`` classes
+- Create separate detector instances in ``NIRCam`` class
+
+
+-----------------------

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2017 Jarron Leisenring
+Copyright (c) 2017 Jarron Leisenring & contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -0,0 +1 @@
+include LICENSE

README.md

@@ -8,12 +8,13 @@ pyNRC - A JWST NIRCam ETC
 **!!Under Development!!**
 
 pyNRC is a set of Python-based tools for planning observations with JWST NIRCam, 
-such as an ETC, ~~rudimentary overhead calculator~~ (TBI), and simple image slope 
-simulator. 
-pyNRC works for a vareity NIRCam observing modes including direct imaging, 
+such as an ETC, ~~rudimentary overhead calculator~~ (TBI), simple image slope 
+simulator, and full-blown DMS simulator.
+
+The module works for a vareity NIRCam observing modes including direct imaging, 
 coronagraphic imaging, slitless grism spectroscopy, ~~DHS observations~~ (TBI), 
 and weak lens imaging.
-All PSFs are generated via WebbPSF (https://webbpsf.readthedocs.io/en/stable/) to reproduce 
+All PSFs are generated via WebbPSF (https://webbpsf.readthedocs.io) to reproduce 
 realistic JWST images and spectra.
 
 **Note**: pyNRC allows for more modes than are officially allowed by the Observatory,
@@ -43,15 +44,11 @@ startup file, such as ``.bashrc``:
 
 - ``export PYNRC_PATH="/Users/Bob/pynrc_data/"``
 
-You can grab the required data files at: http://mips.as.arizona.edu/~jleisenring/pynrc/pynrc_data_v0.5.0.tar. One of the directories includes speckle maps for computing contrasts. These files can either be computed directly via the generate_speckle_maps.ipynb or downloaded at http://mips.as.arizona.edu/~jleisenring/pynrc/speckle_maps.tar.
+You can grab the required data files at: http://mips.as.arizona.edu/~jleisenring/pynrc/pynrc_data_v0.6.0.tar. 
 
 ## Requirements
 
-+ Python 2.7.x (3.x compatability not guaranteed, but vetting welcome!)
-+ WebbPSF >=0.5.0 (https://pythonhosted.org/webbpsf/)
-+ Astropy >=1.2.0 (http://www.astropy.org/)
-+ Pysynphot >=0.9.8.2 (https://pysynphot.readthedocs.io)
-+ Others???
-
-#### Recommended
-+ Seaborn >=0.7.0 (https://seaborn.pydata.org/)
++ Python >=2.7.0 or >=3.5
++ WebbPSF >=0.6.0 (https://pythonhosted.org/webbpsf/)
++ Astropy >=1.3.0 (http://www.astropy.org/)
++ Pysynphot >=0.9.8.0 (https://pysynphot.readthedocs.io)

TODO.rst

@@ -0,0 +1,44 @@
+Planned Updates
+---------------
+
+FoV aware positions
++++++++++++++++++++
+    - Background roll off at grism edges
+    - Filter location relative offsets
+    - SIAF info
+    - Subarray positions
+    - SCA Gaps and Module gaps
+
+Detector updates in ngNRC.py
+++++++++++++++++++++++++++++
+    - Pixel non-linearity
+    - Intrapixel Capacitance (IPC)
+    - Post-pixel Coupling (PPC) due to ADC "smearing"
+    - Persistence/latent image
+    - Optical distortions
+    - QE variations across a pixel's surface
+    - RTN Noise
+    - Flat field variations
+
+PSF Related
++++++++++++
+    - Actual coronagraphic throughput from FITS files
+    - Include dispersion of coronagraph PSF
+    - PSF Jitter options
+    - Bar Mask offsets (using nrc.options['bar_offset'])
+    - PSF convolution based on geometric spot size
+
+Observation Classes
++++++++++++++++++++
+    - Grism time series
+    - Photometric time series (incl. weak lens)
+    - Wide-field grism
+    - Wide field imaging (esp. SW modules)
+
+Miscellaneous
++++++++++++++
+    - Random cosmic ray hits in exposure simulator
+    - Ramp optimizer warning for large number of group loops?
+    - multi-thread ramp optimizer?
+    - DHS mode
+

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = pynrc
+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/api/detector_classes.rst

@@ -0,0 +1,7 @@
+Detector Classes
+================
+
+.. toctree::
+
+    pynrc.DetectorOps.rst
+    pynrc.multiaccum.rst

docs/api/math_tools.rst

@@ -0,0 +1,111 @@
+.. currentmodule:: pynrc
+
+Math Tools
+==============
+
+.. rubric:: Coordinates Summary
+
+.. autosummary::
+
+    ~pynrc.maths.coords.dist_image
+    ~pynrc.maths.coords.xy_to_rtheta
+    ~pynrc.maths.coords.rtheta_to_xy
+    ~pynrc.maths.coords.xy_rot
+    ~pynrc.maths.coords.Tel2Sci_info
+    ~pynrc.maths.coords.det_to_V2V3
+    ~pynrc.maths.coords.V2V3_to_det
+    ~pynrc.maths.coords.plotAxes
+
+.. rubric:: Image Manipulation Summary
+
+.. autosummary::
+
+    ~pynrc.maths.image_manip.hist_indices
+    ~pynrc.maths.image_manip.binned_statistic
+    ~pynrc.maths.image_manip.frebin
+    ~pynrc.maths.image_manip.fshift
+    ~pynrc.maths.image_manip.fourier_imshift
+    ~pynrc.maths.image_manip.shift_subtract
+    ~pynrc.maths.image_manip.align_LSQ
+    ~pynrc.maths.image_manip.scale_ref_image
+    ~pynrc.maths.image_manip.optimal_difference
+    ~pynrc.maths.image_manip.pad_or_cut_to_size
+    ~pynrc.maths.image_manip.fix_nans_with_med
+
+.. rubric:: Polynomial Fitting Summary
+
+.. autosummary::
+
+    ~pynrc.maths.fast_poly.jl_poly_fit
+    ~pynrc.maths.fast_poly.jl_poly
+
+.. rubric:: Robust Summary
+
+.. autosummary::
+
+    ~pynrc.maths.robust.biweightMean
+    ~pynrc.maths.robust.checkfit
+    ~pynrc.maths.robust.linefit
+    ~pynrc.maths.robust.mean
+    ~pynrc.maths.robust.medabsdev
+    ~pynrc.maths.robust.mode
+    ~pynrc.maths.robust.polyfit
+    ~pynrc.maths.robust.std
+
+
+----------------------------
+
+``pynrc.maths.coords``
+--------------------------
+
+.. autofunction:: pynrc.maths.coords.dist_image
+.. autofunction:: pynrc.maths.coords.xy_to_rtheta
+.. autofunction:: pynrc.maths.coords.rtheta_to_xy
+.. autofunction:: pynrc.maths.coords.xy_rot
+.. autofunction:: pynrc.maths.coords.Tel2Sci_info
+.. autofunction:: pynrc.maths.coords.det_to_V2V3
+.. autofunction:: pynrc.maths.coords.V2V3_to_det
+.. autofunction:: pynrc.maths.coords.plotAxes
+
+----------------------------
+
+``pynrc.maths.image_manip``
+----------------------------
+
+.. autofunction:: pynrc.maths.image_manip.hist_indices
+.. autofunction:: pynrc.maths.image_manip.binned_statistic
+.. autofunction:: pynrc.maths.image_manip.frebin
+.. autofunction:: pynrc.maths.image_manip.fshift
+.. autofunction:: pynrc.maths.image_manip.fourier_imshift
+.. autofunction:: pynrc.maths.image_manip.shift_subtract
+.. autofunction:: pynrc.maths.image_manip.align_LSQ
+.. autofunction:: pynrc.maths.image_manip.scale_ref_image
+.. autofunction:: pynrc.maths.image_manip.optimal_difference
+.. autofunction:: pynrc.maths.image_manip.pad_or_cut_to_size
+.. autofunction:: pynrc.maths.image_manip.fix_nans_with_med
+
+----------------------------
+
+``pynrc.maths.fast_poly``
+--------------------------
+
+.. autofunction:: pynrc.maths.fast_poly.jl_poly_fit
+.. autofunction:: pynrc.maths.fast_poly.jl_poly
+
+----------------------------
+
+``pynrc.maths.robust``
+----------------------------
+
+Small collection of robust statistical estimators based on functions from
+Henry Freudenriech (Hughes STX) statistics library (called ROBLIB) that have
+been incorporated into the AstroIDL User's Library.
+
+.. autofunction:: pynrc.maths.robust.biweightMean
+.. autofunction:: pynrc.maths.robust.checkfit
+.. autofunction:: pynrc.maths.robust.linefit
+.. autofunction:: pynrc.maths.robust.mean
+.. autofunction:: pynrc.maths.robust.medabsdev
+.. autofunction:: pynrc.maths.robust.mode
+.. autofunction:: pynrc.maths.robust.polyfit
+.. autofunction:: pynrc.maths.robust.std

docs/api/nghxrg.rst

@@ -0,0 +1,23 @@
+nghxrg
+=================
+
+.. currentmodule:: pynrc.simul.nghxrg
+
+.. autoclass:: pynrc.simul.nghxrg.HXRGNoise
+   :show-inheritance:
+
+   .. rubric:: Methods Summary
+
+   .. autosummary::
+
+      ~pynrc.simul.nghxrg.HXRGNoise.message
+      ~pynrc.simul.nghxrg.HXRGNoise.mknoise
+      ~pynrc.simul.nghxrg.HXRGNoise.pink_noise
+      ~pynrc.simul.nghxrg.HXRGNoise.white_noise
+
+   .. rubric:: Methods Documentation
+
+   .. automethod:: message
+   .. automethod:: mknoise
+   .. automethod:: pink_noise
+   .. automethod:: white_noise

docs/api/ngnrc.rst

@@ -0,0 +1,16 @@
+ngNRC
+=================
+
+.. currentmodule:: pynrc.simul.ngNRC
+
+.. rubric:: Summary
+
+.. autosummary::
+
+    ~pynrc.simul.ngNRC.SCAnoise
+    ~pynrc.simul.ngNRC.slope_to_ramp
+
+.. rubric:: Documentation
+
+.. autofunction:: pynrc.simul.ngNRC.SCAnoise
+.. autofunction:: pynrc.simul.ngNRC.slope_to_ramp

docs/api/nrc_utils.rst

@@ -0,0 +1,41 @@
+.. currentmodule:: pynrc
+
+NIRCam Tools
+============
+
+.. rubric:: Functions Summary
+
+.. autosummary::
+
+    ~nrc_utils.read_filter
+    ~nrc_utils.psf_coeff
+    ~nrc_utils.wfed_coeff
+    ~nrc_utils.gen_image_coeff
+    ~nrc_utils.bg_sensitivity
+    ~nrc_utils.sat_limit_webbpsf
+    ~nrc_utils.pix_noise
+    ~nrc_utils.channel_select
+    ~nrc_utils.grism_res
+    ~nrc_utils.build_mask
+    ~nrc_utils.coron_trans
+    ~nrc_utils.offset_bar
+    ~nrc_utils.config2
+    ~nrc_utils.create_detops
+
+
+.. rubric:: Documentation
+
+.. autofunction:: pynrc.nrc_utils.read_filter
+.. autofunction:: pynrc.nrc_utils.psf_coeff
+.. autofunction:: pynrc.nrc_utils.wfed_coeff
+.. autofunction:: pynrc.nrc_utils.gen_image_coeff
+.. autofunction:: pynrc.nrc_utils.bg_sensitivity
+.. autofunction:: pynrc.nrc_utils.sat_limit_webbpsf
+.. autofunction:: pynrc.nrc_utils.pix_noise
+.. autofunction:: pynrc.nrc_utils.channel_select
+.. autofunction:: pynrc.nrc_utils.grism_res
+.. autofunction:: pynrc.nrc_utils.build_mask
+.. autofunction:: pynrc.nrc_utils.coron_trans
+.. autofunction:: pynrc.nrc_utils.offset_bar
+.. autofunction:: pynrc.nrc_utils.config2
+.. autofunction:: pynrc.nrc_utils.create_detops

docs/api/obs_classes.rst

@@ -0,0 +1,7 @@
+Observation Classes
+===================
+
+.. toctree::
+
+    pynrc.NIRCam.rst
+    pynrc.obs_coronagraphy.rst