Merge branch 'master' of https://github.com/JarronL/pynrc

TODO.rst

@@ -3,7 +3,7 @@ Planned Updates
 
 FoV aware positions
 +++++++++++++++++++
-    - Correct coronagraph field locations (CIRC vs BAR)
+    - Correct coronagraph field locations depending on Lyot optical wedge
     - Background roll off at grism edges
     - Filter location relative offsets
     - SIAF info
@@ -15,6 +15,8 @@ Detector updates in ngNRC.py
     - Pixel non-linearity
     - Intrapixel Capacitance (IPC)
     - Post-pixel Coupling (PPC) due to ADC "smearing"
+    - Pixel glow based on subarray size
+    - Charge diffusion (esp for saturated pixels)
     - Persistence/latent image
     - Optical distortions
     - QE variations across a pixel's surface
@@ -23,15 +25,16 @@ Detector updates in ngNRC.py
 
 PSF Related
 +++++++++++
+    - Coronagraph target acquisition uncertainties
+    - Small grid dither strategy in coronagraphic observations
     - Actual coronagraphic throughput from FITS files
-    - Include dispersion of coronagraph PSF
     - More PSF Jitter options
     - PSF convolution based on geometric spot size
 
 Observation Classes
 +++++++++++++++++++
-    - Grism time series
     - Photometric time series (incl. weak lens)
+    - Grism time series
     - Wide-field grism
     - Wide field imaging (esp. SW modules)
 

pynrc/WFE_interpolation.py

@@ -220,5 +220,82 @@
 #     plt.ylim([Y.min(),Y.max()])
 #     plt.axes().set_aspect('equal', 'datalim')
 
-# names = ['Guider1', 'Guider2', 'MIRI', 'NIRCamLWA', 'NIRCamLWB', 
-# 'NIRCamSWA', 'NIRCamSWB', 'NIRISS', 'NIRSpec']
+
+
+
+names = ['Guider1', 'Guider2', 'MIRI', 'NIRISS', 'NIRSpec',
+         'NIRCamLWA', 'NIRCamLWB', 'NIRCamSWA', 'NIRCamSWB']
+
+from pysiaf.siaf import plot_main_apertures
+
+fig, axes = plt.subplots(3,1, figsize=(8,10))
+axes = axes.flatten()
+
+lookup_name = 'NIRSpec'
+
+for lookup_name in names:
+    ztable = ztable_full[ztable_full['instrument'] == lookup_name]
+
+    v2 = ztable['V2']
+    v3 = ztable['V3']
+
+    i=4
+    zkey = 'Zernike_{}'.format(i)
+    zvals = ztable[zkey]
+
+
+    dstep = 1. / 60. # 1" steps
+    xgrid = np.arange(v2.min(), v2.max()+dstep, dstep)
+    ygrid = np.arange(v3.min(), v3.max()+dstep, dstep)
+    X, Y = np.meshgrid(xgrid,ygrid)
+
+    # Cubic interpolation of all points
+    zgrid = griddata((v2, v3), zvals, (X, Y), method='cubic')
+    zmin, zmax = np.nanmin(zgrid), np.nanmax(zgrid)
+
+    ax = axes[0]
+    extent = np.array([xgrid.min(),xgrid.max(),ygrid.min(),ygrid.max()]) * 60
+    ax.imshow(zgrid, extent=extent, vmin=zmin, vmax=zmax)
+    ax.plot(v2*60, v3*60, ls='none', marker='x', color='C1')
+    ax.set_title("griddata with method='cubic'")
+
+
+    # There will be some NaNs along the border that need to be replaced
+    ind_nan = np.isnan(zgrid)
+    # Remove rows/cols 1 by 1 until no NaNs
+    zgrid2 = zgrid
+    ygrid2 = ygrid
+    xgrid2 = xgrid
+    while np.isnan(zgrid2.sum()):
+        zgrid2 = zgrid2[1:-1,1:-1]
+        ygrid2 = ygrid2[1:-1]
+        xgrid2 = xgrid2[1:-1]
+
+    ax = axes[1]
+    extent = np.array([xgrid2.min(),xgrid2.max(),ygrid2.min(),ygrid2.max()]) * 60
+    ax.imshow(zgrid2, extent=extent, vmin=zmin, vmax=zmax)
+    ax.plot(v2*60, v3*60, ls='none', marker='x', color='C1')
+    ax.set_title("Trimmed for RegularGridInterpolator")
+
+
+    # Create regular grid interpolator function for extrapolation of NaN's
+    func = RegularGridInterpolator((ygrid2,xgrid2), zgrid2, method='linear',
+                                   bounds_error=False, fill_value=None)
+
+    # Replace NaNs
+    pts = np.array([Y[ind_nan], X[ind_nan]]).transpose()
+    zgrid[ind_nan] = func(pts)
+
+    ax = axes[2]
+    extent = np.array([xgrid.min(),xgrid.max(),ygrid.min(),ygrid.max()]) * 60
+    ax.imshow(zgrid, extent=extent, vmin=zmin, vmax=zmax)
+    ax.plot(v2*60, v3*60, ls='none', marker='x', color='C1')
+    ax.set_title("NaN replacement")
+
+for ax in axes:
+    plot_main_apertures(ax=ax, fill=False, mark_ref=False)
+    ax.set_xlim([600,-600])
+    ax.set_ylim([-800,-250])
+
+fig.tight_layout()
+

pynrc/apertures.txt

@@ -0,0 +1,227 @@
+# Full instrument aperture
+'NRCALL_FULL'
+
+# SW module Apertures
+'NRCAS_FULL'
+'NRCBS_FULL'
+
+# Mod A SCAs
+'NRCA1_FULL'
+'NRCA2_FULL'
+'NRCA3_FULL'
+'NRCA4_FULL'
+'NRCA5_FULL'
+
+# Mod B SCAs
+'NRCB1_FULL'
+'NRCB2_FULL'
+'NRCB3_FULL'
+'NRCB4_FULL'
+'NRCB5_FULL'
+
+# Mod B SW/LW full frame point source obs
+'NRCB1_FULLP'
+'NRCB5_FULLP'
+
+# 160x160 direct imaging subarray
+'NRCA1_SUB160'
+'NRCA2_SUB160'
+'NRCA3_SUB160'
+'NRCA4_SUB160'
+'NRCA5_SUB160'
+'NRCB1_SUB160'
+'NRCB2_SUB160'
+'NRCB3_SUB160'
+'NRCB4_SUB160'
+'NRCB5_SUB160'
+
+# 320x320 subarray
+'NRCA1_SUB320'
+'NRCA2_SUB320'
+'NRCA3_SUB320'
+'NRCA4_SUB320'
+'NRCA5_SUB320'
+'NRCB1_SUB320'
+'NRCB2_SUB320'
+'NRCB3_SUB320'
+'NRCB4_SUB320'
+'NRCB5_SUB320'
+
+# 6400x640 subarray
+'NRCA1_SUB640'
+'NRCA2_SUB640'
+'NRCA3_SUB640'
+'NRCA4_SUB640'
+'NRCA5_SUB640'
+'NRCB1_SUB640'
+'NRCB2_SUB640'
+'NRCB3_SUB640'
+'NRCB4_SUB640'
+'NRCB5_SUB640'
+
+# Grism STRIPE observations (filter dependent)
+'NRCA5_GRISM256_F322W2'
+'NRCA5_GRISM128_F322W2'
+'NRCA5_GRISM64_F322W2'
+'NRCA5_GRISM256_F277W'
+'NRCA5_GRISM128_F277W'
+'NRCA5_GRISM64_F277W'
+'NRCA5_GRISM256_F356W'
+'NRCA5_GRISM128_F356W'
+'NRCA5_GRISM64_F356W'
+'NRCA5_GRISM256_F444W'
+'NRCA5_GRISM128_F444W'
+'NRCA5_GRISM64_F444W'
+
+# Grism Full frame observations (filter dependent)
+'NRCA5_GRISM_F322W2'
+'NRCA5_GRISM_F277W'
+'NRCA5_GRISM_F356W'
+'NRCA5_GRISM_F444W'
+
+# Time series grism observations
+'NRCA1_GRISMTS'
+'NRCA1_GRISMTS256'
+'NRCA1_GRISMTS128'
+'NRCA1_GRISMTS64'
+'NRCA3_GRISMTS'
+'NRCA3_GRISMTS256'
+'NRCA3_GRISMTS128'
+'NRCA3_GRISMTS64'
+
+# Time series grism target acquisition
+'NRCA5_TAGRISMTS32'
+'NRCA5_TAGRISMTS_SCI_F322W2'
+'NRCA5_TAGRISMTS_SCI_F444W'
+
+# Wide field slitless
+'NRCA5_GRISMC_WFSS'
+'NRCA5_GRISMR_WFSS'
+'NRCALL_GRISMC_WFSS'
+'NRCALL_GRISMR_WFSS'
+'NRCB5_GRISMC_WFSS'
+'NRCB5_GRISMR_WFSS'
+
+
+# DHS PIL
+'NRCA3_DHSPIL'
+'NRCA3_DHSPIL_SUB96'
+'NRCA3_DHSPIL_WEDGES'
+'NRCB4_DHSPIL'
+'NRCB4_DHSPIL_SUB96'
+'NRCB4_DHSPIL_WEDGES'
+
+# Field points for wavefront sensing
+'NRCA3_FP1'
+'NRCA3_FP1_SUB8'
+'NRCA3_FP1_SUB64'
+'NRCA3_FP2MIMF'
+'NRCA1_FP3MIMF'
+'NRCA2_FP4MIMF'
+'NRCA4_FP5MIMF'
+'NRCB4_FP1'
+'NRCB4_FP1_SUB8'
+'NRCB4_FP1_SUB64'
+'NRCB4_FP2MIMF'
+'NRCB2_FP3MIMF'
+'NRCB1_FP4MIMF'
+'NRCB3_FP5MIMF'
+
+# Point source subarrays
+'NRCA3_SUB64P'
+'NRCA3_SUB160P'
+'NRCA3_SUB400P'
+'NRCA5_SUB64P'
+'NRCA5_SUB160P'
+'NRCA5_SUB400P'
+'NRCB1_SUB64P'
+'NRCB1_SUB160P'
+'NRCB1_SUB400P'
+'NRCB5_SUB64P'
+'NRCB5_SUB160P'
+'NRCB5_SUB400P'
+
+# Target acq for point source imaging?
+'NRCB5_TAPSIMG32'
+
+
+# Module A masks and ND Squares
+'NRCA2_MASK210R'
+'NRCA5_MASK335R'
+'NRCA5_MASK430R'
+'NRCA4_MASKSWB'
+'NRCA5_MASKLWB'
+'NRCA2_TAMASK210R'
+'NRCA5_TAMASK335R'
+'NRCA5_TAMASK430R'
+'NRCA4_TAMASKSWB'
+'NRCA5_TAMASKLWB'
+'NRCA5_TAMASKLWBL'
+'NRCA4_TAMASKSWBS'
+
+# Module B masks and ND Squares
+'NRCB1_MASK210R'
+'NRCB5_MASK335R'
+'NRCB5_MASK430R'
+'NRCB3_MASKSWB'
+'NRCB5_MASKLWB'
+'NRCB1_TAMASK210R'
+'NRCB5_TAMASK335R'
+'NRCB5_TAMASK430R'
+'NRCB3_TAMASKSWB'
+'NRCB5_TAMASKLWB'
+'NRCB5_TAMASKLWBL'
+'NRCB3_TAMASKSWBS'
+
+# Module A faint target acq
+'NRCA2_FSTAMASK210R'
+'NRCA4_FSTAMASKSWB'
+'NRCA5_FSTAMASKLWB'
+'NRCA5_FSTAMASK335R'
+'NRCA5_FSTAMASK430R'
+
+# Module A SWBar wavelength reference points
+'NRCA4_MASKSWB_F182M'
+'NRCA4_MASKSWB_F187N'
+'NRCA4_MASKSWB_F210M'
+'NRCA4_MASKSWB_F212N'
+'NRCA4_MASKSWB_F200W'
+'NRCA4_MASKSWB_NARROW'
+
+
+# Module A LWBar wavelength reference points
+'NRCA5_MASKLWB_F250M'
+'NRCA5_MASKLWB_F300M'
+'NRCA5_MASKLWB_F277W'
+'NRCA5_MASKLWB_F335M'
+'NRCA5_MASKLWB_F360M'
+'NRCA5_MASKLWB_F356W'
+'NRCA5_MASKLWB_F410M'
+'NRCA5_MASKLWB_F430M'
+'NRCA5_MASKLWB_F460M'
+'NRCA5_MASKLWB_F480M'
+'NRCA5_MASKLWB_F444W'
+'NRCA5_MASKLWB_NARROW'
+
+# Module A Full Frame
+'NRCA2_FULL_MASK210R'
+'NRCA5_FULL_MASK335R'
+'NRCA5_FULL_MASK430R'
+'NRCA4_FULL_MASKSWB'
+'NRCA4_FULL_MASKSWB_F182M'
+'NRCA4_FULL_MASKSWB_F187N'
+'NRCA4_FULL_MASKSWB_F210M'
+'NRCA4_FULL_MASKSWB_F212N'
+'NRCA4_FULL_MASKSWB_F200W'
+'NRCA5_FULL_MASKLWB'
+'NRCA5_FULL_MASKLWB_F250M'
+'NRCA5_FULL_MASKLWB_F300M'
+'NRCA5_FULL_MASKLWB_F277W'
+'NRCA5_FULL_MASKLWB_F335M'
+'NRCA5_FULL_MASKLWB_F360M'
+'NRCA5_FULL_MASKLWB_F356W'
+'NRCA5_FULL_MASKLWB_F410M'
+'NRCA5_FULL_MASKLWB_F430M'
+'NRCA5_FULL_MASKLWB_F460M'
+'NRCA5_FULL_MASKLWB_F480M'
+'NRCA5_FULL_MASKLWB_F444W'