Updates to do list in documentation

docs/build/html/_sources/changelog.rst.txt

@@ -71,42 +71,35 @@ v0.1.2 June 2019, R.G. van Holstein:
 To-do high priority
 -------------------
 
-   - Add computation of mean stellar polarization and uncertainty when mean-combining data sets
    - Improve computation of stellar DoLP and AoLP and corresponding uncertainties (standard error of mean) by sampling from Gaussian distributions with Monte Carlo
    - Correct error in computation of photon noise for Q and U images that uses signal in Q and U rather than I_Q and I_U.
-   - Add tool to create plots of I_pol and AoLP from terminal.
-   - Add centering method that minimizes the SSR of the left minus right frames in an aperture centered on the star
    - Make the data reduction work for data taken before approximately May 2015 that do not contain the header keyword indicating the Stokes parameter (using the HWP angle instead)
    - Make IRDAP throw out less files when the order of the Stokes parameters of the files is not Qplus, Qminus, Uplus, Uminus
    - Add possibility to use CENTER-frames with a different exposure time than the OBJECT-frames
    - Add possibility to express contrast curves of extended sources in Jansky/arcsec^2
-   - Improve computation of stellar DoLP and AoLP and corresponding uncertainties by sampling from Gaussian distributions with Monte Carlo
    - Make PDI part more memory efficient by re-using names of cubes
    - Remove bad pixels in frames by setting them to NaN, and when frames are rotating (in PT and FT with derotator offsets) use nanmean to filter bad pixels out
    - Make an overview of the warnings at the end of the log file
-   - Add possibility to crop images when doing ADI to save time
-   - Create contrast curves of final ADI-images 
-   - Add ADI+PCA for polarimetric data reduction of pupil-tracking observations
+   - Add classical ADI for polarimetric data reduction of pupil-tracking observations
    - Add accurate (calibrated) model correction for narrowband filters
    - Add option to apply accurate plate scale and distortion correction for data (especially important for pupil-tracking and bright sources; do we need calibrations?)
-   - For pupil-tracking data mask bad pixel clusters when computing least squares solution to get rid off sectors of bad data; for field-tracking data set bad pixel clusters to NaN   
-
+   - For pupil-tracking data mask bad pixel clusters when computing least squares solution to get rid off sectors of bad data; for field-tracking data set bad pixel clusters to NaN.
 
 To-do low priority
 ------------------
 
-   - Add images and plots aimed at analysis of polarimetric data (R^2 scaling, AoLP arrows in polarized intensity or DoLP images, contrast curves etc.)	
+   - Add computation of mean stellar polarization and uncertainty when mean-combining data sets
+   - Add images and plots aimed at analysis of polarimetric data (R^2 scaling, AoLP arrows in polarized intensity or DoLP images), maybe using terminal commands.	
    - Add option to subtract DARK,BACKGROUND-frames if sky files are lacking (especially important for Ks; test effect first before completely implementing)
+   - Add option to scale the master sky frame to subtract from the object frames (especially for Ks; see also Gallicher et al. 2011)
    - Add option for 'stupid ADI' for field-tracking data with derotator offset and option to subtract 180 deg rotated image if no derotator offset
+   - Create contrast curves of final ADI-images 
    - Make figures with sub-images horizontal, or make multiple lines of left and right images in a single figure   
    - Add options for various methods to shift and rotate images (interpolate, ndimage-fourier, sci-image functions; similar to VIP)
-   - When rotating images, make complete frame still visible to not cut out any parts of the data
    - Improve centering of non-coronagraphic data (center found depends a lot on first PSF and affects Qphi and Uphi images). Perhaps fit coordinates on each PSF, but do the actual shifts with the mean of these fitted values. This has proven to give a more accurate final result. 
+   - Add centering method that minimizes the SSR of the left minus right frames in an aperture centered on the star
    - Test finding of satellite spots of center files when waffle pattern is '+'
    - Add weighted least-squares as option for model correction (depending on image quality or polarimetric efficiency)	
-   - Add multiprocessing for sigma filtering and centering of frames
-   - Add option to scale the master sky frame to subtract from the object frames (especially for Ks; see also Gallicher et al. 2011)
    - Exclude saturated pixels in aperture to determine star polarization (same way as used in function fit_2d_gaussian)
    - Determine star polarization as a function of aperture radius	
    - Add optional RDI for total intensity images	
-   - Make docstrings compliant with accepted conventions and create API doc on website

docs/build/html/changelog.html

@@ -255,47 +255,41 @@ <h2>Changelog<a class="headerlink" href="#changelog" title="Permalink to this he
 <h2>To-do high priority<a class="headerlink" href="#to-do-high-priority" title="Permalink to this headline">¶</a></h2>
 <blockquote>
 <div><ul class="simple">
-<li>Add computation of mean stellar polarization and uncertainty when mean-combining data sets</li>
 <li>Improve computation of stellar DoLP and AoLP and corresponding uncertainties (standard error of mean) by sampling from Gaussian distributions with Monte Carlo</li>
 <li>Correct error in computation of photon noise for Q and U images that uses signal in Q and U rather than I_Q and I_U.</li>
-<li>Add tool to create plots of I_pol and AoLP from terminal.</li>
-<li>Add centering method that minimizes the SSR of the left minus right frames in an aperture centered on the star</li>
 <li>Make the data reduction work for data taken before approximately May 2015 that do not contain the header keyword indicating the Stokes parameter (using the HWP angle instead)</li>
 <li>Make IRDAP throw out less files when the order of the Stokes parameters of the files is not Qplus, Qminus, Uplus, Uminus</li>
 <li>Add possibility to use CENTER-frames with a different exposure time than the OBJECT-frames</li>
 <li>Add possibility to express contrast curves of extended sources in Jansky/arcsec^2</li>
-<li>Improve computation of stellar DoLP and AoLP and corresponding uncertainties by sampling from Gaussian distributions with Monte Carlo</li>
 <li>Make PDI part more memory efficient by re-using names of cubes</li>
 <li>Remove bad pixels in frames by setting them to NaN, and when frames are rotating (in PT and FT with derotator offsets) use nanmean to filter bad pixels out</li>
 <li>Make an overview of the warnings at the end of the log file</li>
-<li>Add possibility to crop images when doing ADI to save time</li>
-<li>Create contrast curves of final ADI-images</li>
-<li>Add ADI+PCA for polarimetric data reduction of pupil-tracking observations</li>
+<li>Add classical ADI for polarimetric data reduction of pupil-tracking observations</li>
 <li>Add accurate (calibrated) model correction for narrowband filters</li>
 <li>Add option to apply accurate plate scale and distortion correction for data (especially important for pupil-tracking and bright sources; do we need calibrations?)</li>
-<li>For pupil-tracking data mask bad pixel clusters when computing least squares solution to get rid off sectors of bad data; for field-tracking data set bad pixel clusters to NaN</li>
+<li>For pupil-tracking data mask bad pixel clusters when computing least squares solution to get rid off sectors of bad data; for field-tracking data set bad pixel clusters to NaN.</li>
 </ul>
 </div></blockquote>
 </div>
 <div class="section" id="to-do-low-priority">
 <h2>To-do low priority<a class="headerlink" href="#to-do-low-priority" title="Permalink to this headline">¶</a></h2>
 <blockquote>
 <div><ul class="simple">
-<li>Add images and plots aimed at analysis of polarimetric data (R^2 scaling, AoLP arrows in polarized intensity or DoLP images, contrast curves etc.)</li>
+<li>Add computation of mean stellar polarization and uncertainty when mean-combining data sets</li>
+<li>Add images and plots aimed at analysis of polarimetric data (R^2 scaling, AoLP arrows in polarized intensity or DoLP images), maybe using terminal commands.</li>
 <li>Add option to subtract DARK,BACKGROUND-frames if sky files are lacking (especially important for Ks; test effect first before completely implementing)</li>
+<li>Add option to scale the master sky frame to subtract from the object frames (especially for Ks; see also Gallicher et al. 2011)</li>
 <li>Add option for ‘stupid ADI’ for field-tracking data with derotator offset and option to subtract 180 deg rotated image if no derotator offset</li>
+<li>Create contrast curves of final ADI-images</li>
 <li>Make figures with sub-images horizontal, or make multiple lines of left and right images in a single figure</li>
 <li>Add options for various methods to shift and rotate images (interpolate, ndimage-fourier, sci-image functions; similar to VIP)</li>
-<li>When rotating images, make complete frame still visible to not cut out any parts of the data</li>
 <li>Improve centering of non-coronagraphic data (center found depends a lot on first PSF and affects Qphi and Uphi images). Perhaps fit coordinates on each PSF, but do the actual shifts with the mean of these fitted values. This has proven to give a more accurate final result.</li>
+<li>Add centering method that minimizes the SSR of the left minus right frames in an aperture centered on the star</li>
 <li>Test finding of satellite spots of center files when waffle pattern is ‘+’</li>
 <li>Add weighted least-squares as option for model correction (depending on image quality or polarimetric efficiency)</li>
-<li>Add multiprocessing for sigma filtering and centering of frames</li>
-<li>Add option to scale the master sky frame to subtract from the object frames (especially for Ks; see also Gallicher et al. 2011)</li>
 <li>Exclude saturated pixels in aperture to determine star polarization (same way as used in function fit_2d_gaussian)</li>
 <li>Determine star polarization as a function of aperture radius</li>
 <li>Add optional RDI for total intensity images</li>
-<li>Make docstrings compliant with accepted conventions and create API doc on website</li>
 </ul>
 </div></blockquote>
 </div>