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@simontorres simontorres released this Aug 19, 2019

  • Bugs fixed

    • Bias process was not fully ignored when --ignore-bias was used [#289].
    • pandas version was not specified in environment.yml [#288, #290]
    • Target extraction failed for low signal targets because background subtraction
      was being ignored at the step of actually identifying targets.
  • Install instructions updated [#290]

  • Moved static methods from ImageProcessor to core.

  • Added function to validate ccd regions using regular expressions.

  • Using lamps keywords to select reference lamps.

  • Replaced target_stddev by target_fwhm in function extract and extract_fractional.

  • Replaced nsigmas by nfwhm everywhere.

  • Added argument --background-threshold with default value 3.

  • Added argument --fit-targets-with with options moffat and gaussian.

Assets 2

@simontorres simontorres released this Oct 26, 2018 · 115 commits to master since this release

  • Bugs removed:

    • If there was more than one lamp for a science target the lamp recorded as used
      was one of them only.
    • A percentage symbols was added to the help of --saturation argument, this
      caused a crash when redccd -h or redccd --help was used.
  • Numpy is fixed to the version 1.15.2 until further notice.

  • Reference lamps now get the extraction window added to the end of the file name.
    This is to avoid overwritting the lamps when they were used for more than one target.

  • DCR install script is now more advanced and requires a virtual environment to work on.

  • Added SOAR Logo to ReadTheDocs page.

  • Changed install instruction with exact steps and commands instead of
    referencing documentation.

  • Improved method to detect saturated images. Added a table with the half full
    well
    for all the readout modes possible and created a method to easily
    retrieve the value. This is a big improvement since in earlier versions the
    saturation limit was set to 65000 ADU regardless the input data and the user
    had to set a different one using the argument --saturation.

  • Repurposed the --saturation command line argument, now is used to define
    the percentage of pixels above the saturation level, which for simplicity is
    the value of half full well. A default value of 1 percent was set as default.

  • Added record information of target trace into the header and logs.

  • Added record of background extraction regions into the header and logs.

  • Made all plots full screen and the images using the gray cmap.

  • Trace information is printed in the logs and also is recorded in the image's
    header

  • Added sigma clipping to target tracing functions

Assets 2

@simontorres simontorres released this Oct 5, 2018 · 195 commits to master since this release

  • Project and package renamed to goodman_pipeline this is because the
    previous was too generic. Now we have this structure:

      goodman_pipeline/
         docs/
         goodman_pipeline/
            core/
            images/
            ..etc
         setup.py
         ..etc
  • Bugs Fixed:

    • :class:~pandas.DataFrame index is unusable when partial parts are eliminated.
      Added index_reset(drop=True)
    • Data conversion from string to integer needed to be converted to float first.
    • For low SNR data there was confusion of noise with targets, added a median
      filter and increased the the order value of peak detection.
  • Created several new keywords:
    GSP_EXTR:
    Extraction window at the first column.
    GSP_SCTR:
    Used for extracted comparison lamps, contains the name of the file of
    science target that the lamp was extracted for.
    GSP_LAMP:
    For science targets, it records the name of the lamp used for the wavelength
    calibration.

  • "Sliding" cross correlation window (to trace non-linearity of wavelength
    solution) is set to the maximum value between the length of the lamp spectrum
    in pixels and four times the global cross correlation of the reference lamp to
    the new one.

  • Iterations in sigma clipping of differences between obtained wavelength
    values and laboratory values was increased from 1 to 3. This is for removing
    bad fitted lines and also RMS error calculation.

  • Gaussian Kernel size for reference lamp convolution is now dependent on slit size and binning

  • Added reference lamps for all gratings and their modes except 1200M0

  • Created script install_dcr.sh

  • Increased code coverage

  • Eliminated None elements in list of instances of :class:pipeline.core.core.NightDataContainer

  • Improved several logging messages

    • In general, it informs more, when it does an action and when it does not.
      What files are discarded,
    • Debugging plots are more complete for identify_targets.
  • Created new argument --debug-plot dedicated for graphical debugging, the
    old --debug will show additional messages but will not produce any
    graphical output.

  • Removed ability to process several folders in sequence, now the pipeline has to
    be run for each folder separately.

Assets 2

@simontorres simontorres released this Aug 23, 2018 · 290 commits to master since this release

  • Bugs Fixed:

    • Added clean exit when pipeline is unable to determine instrument or
      technique used.
    • Conversion from string to integer not always works, added intermediate float
      conversion.
    • Abrupt exit when there were non-fits-compliant keywords. Now it attempts to
      fix them all automatically and warns the user. Also, it ends the execution
      and informs the user to try again.
  • Removed unused code and tools.

  • Relocated module check_version from pipeline.tools` to pipeline/core.

  • Implemented Authorized GitHub API access and added actual version check

  • Moved command line interface from goodman/bin/ to goodman/pipeline/scripts/

  • Specified version of cython to be able to build.

  • Added reference lamps for all usable modes for the grating 600 l/mm

  • Created method to use automatic keyword fix from ccdproc.

  • Improved help information of arguments

  • Documentation updates

Assets 2
Aug 23, 2018

v

Merge pull request #215 from simontorres/Release_v1_1_1
ready for release v1.1.1

@simontorres simontorres released this Jul 24, 2018 · 319 commits to master since this release

  • Bugs fixed

    • --keep-cosmic-file would work for dcr but not for lacosmic
  • Changed organization of ReadTheDocs information

    • New structure
    • Added references to external packages
    • This page is the single place to add changes information. CHANGES.md still
      exist but contains a link here.
  • Added --version argument.

  • Improved help information for some arguments.

  • Implemented astroscrappy's LACosmic method

  • removed ccdproc's :func:~ccdproc.cosmicray_lacosmic.

  • created default method for cosmic ray rejection.

    • For binning 1x1 default is dcr
    • For binning 2x2 default is lacosmic
    • For binning 3x3 default is lacosmic

methods dcr, lacosmic or none can still be forced by using
--cosmic <method>

Assets 2

@simontorres simontorres released this Jul 11, 2018 · 371 commits to master since this release

This release fixes the broken v1.0.2

  • Bugs fixed
    • programatically access to the version number did not work because it was based purely on setup.cfg now setup.py has a function that creates the file pipeline/version.py which is accessed by pipeline/__init__.py
    • File naming was making some file disappear by being overwritten for files that contained more than one target the next file name would match the previous one. A differentiator was added.
Assets 2
Pre-release

@simontorres simontorres released this Jul 10, 2018 · 379 commits to master since this release

  • Removed module goodman/pipeline/info.py and placed all metadata in goodman/setup.cfg.

  • Several updates to documentation

    • Added comment on how to organize data on soardata3.
    • Added link to licence on footer.
    • User manual now is in ReadTheDocs and no longer available as a pdf.
    • Improved information on debug plots
  • Bugs Fixed.

    • fixed GSP_FNAM value for reference lamps
    • Spectral limit calculation by including binning into the equation
    • Included binning in the calculation of the wavelength solution
    • Corrected messages and conditions under which the prefix for cosmic ray rejection is used
    • Image combination call and messages
  • Other additions

    • Added lookup table dcr.par file generator and found optimal parameters for Red camera and binning 2x2
Assets 2
Apr 29, 2018
Built v1.0.0 in .tar.gz and in .zip formats.

@b1quint b1quint released this Apr 29, 2018 · 459 commits to master since this release

  • redccd and redspec now working.
  • Supports Goodman data obtained since March 2018.
  • Automatic wavelength calibration for the 400 l/mm in the 400 M1 and 400 M2 modes.
Assets 2
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