spacetelescope · FDauphin · Sep 17, 2021
@@ -8,11 +8,11 @@ WFC3TOOLS
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
     :target: http://www.astropy.org
     :alt: Powered by Astropy Badge
-
 
-For more information please see the `online documentation <http://wfc3tools.readthedocs.io/>`_
 
-You can also display the docs locally after install, import wfc3tools and then issue the following command to display the help docs in your local browser:
+For more information please see the `online documentation <http://wfc3tools.readthedocs.io/>`_.
+
+You can also display the docs locally after install, import ``wfc3tools`` and then issue the following command to display the help docs in your local browser:
 
 ::
 
@@ -37,12 +37,12 @@ leave a comment and we will be happy to assist.   New contributions and
 contributors are very welcome!
 
 New to github or open source projects?  If you are unsure about where to start
-or haven't used github before, please feel free to contact `@sosey`.
+or haven't used github before, please feel free to contact `HST Help Desk <https://stsci.service-now.com/hst>`_.
 
 Feedback and feature requests?   Is there something missing you would like
-to see?  Please open an issue or send an email to  `@sosey`.
+to see?  Please open an issue or contact `HST Help Desk <https://stsci.service-now.com/hst>`_.
 
-wfc3tools follows the `Astropy Code of Conduct`_ and strives to provide a
+``wfc3tools`` follows the `Astropy Code of Conduct`_ and strives to provide a
 welcoming community to all of our users and contributors.
 
 Want more information about how to make a contribution?  Take a look at
@@ -52,7 +52,7 @@ the the astropy `contributing`_ and `developer`_ documentation.
 License
 -------
 
-wfc3tools is licensed under a 3-clause BSD style license (see the ``LICENSE.txt`` file).
+``wfc3tools`` is licensed under a 3-clause BSD style license (see the ``LICENSE.txt`` file).
 
 .. _AstroPy: http://www.astropy.org/
 .. _contributing: http://docs.astropy.org/en/stable/index.html#contributing

@@ -7,7 +7,7 @@
 WFC3 Python User Tools
 ===============================================
 See the team website  http://www.stsci.edu/hst/wfc3/ and the
-`WFC3 Data Handbook <http://www.stsci.edu/hst/wfc3/documents/handbooks/currentDHB/>`_ for more information.
+`WFC3 Data Handbook <https://hst-docs.stsci.edu/wfc3dhb>`_ for more information.
 
 
 ============================

@@ -8,7 +8,7 @@ calwf3
 
 .. note::
 
-    During automatic pipeline processing by the STScI archive, `Astrodrizzle` follows `calwf3`. All calibrated images are corrected for geometric distortion and associated sets of dithered images are combined into a single product. See the WFC3 Data Handbook for more information, or `Astrodrizzle <http://www.stsci.edu/hst/HST_overview/drizzlepac/>`_ .
+    During automatic pipeline processing by the STScI archive, `Astrodrizzle` follows `calwf3`. All calibrated images are corrected for geometric distortion and associated sets of dithered images are combined into a single product. See the WFC3 Data Handbook for more information, or `Astrodrizzle <https://www.stsci.edu/scientific-community/software/drizzlepac.html>`_ .
 
 
 Where to Find calwf3
@@ -17,10 +17,10 @@ Where to Find calwf3
 `calwf3` is part of HSTCAL package, which can be downloaded separately from its GIT repository in the `Spacetelescope <https://github.com/spacetelescope/hstcal>`_ area.  It's binaries are also installed along with the STScI distributed package `Astroconda <http://astroconda.readthedocs.io/en/latest/installation.html>`_ .
 
 
-A detailed description of the improvements in `calwf3 v3.3`, which is more generally referred to as the UVIS2.0 update, can be found in the `February 22, 2016 issue of the STAN <http://www.stsci.edu/hst/wfc3/documents/newsletters/STAN_02_23_2016#STANIssue22-CALWF3Version3.3>`_.
+A detailed description of the improvements in `calwf3 v3.3`, which is more generally referred to as the UVIS2.0 update, can be found in the `February 22, 2016 issue of the STAN <https://www.stsci.edu/contents/news/wfc3-stans/wfc3-stan-issue-22-february-2016.html#h3-CK-04ec3e61-697b-4ea2-9259-75ae75075f63>`_.
 
-The current WFC3 Data Handbook can be found at  http://www.stsci.edu/hst/wfc3/documents/handbooks/currentDHB/ .
-In the meantime, if you have questions not answered in this documentation, please contact STScI Help Desk (help[at]stsci.edu).
+The current WFC3 Data Handbook can be found at  https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/wfc3/_documents/wfc3_dhb.pdf .
+In the meantime, if you have questions not answered in this documentation, please contact STScI Help Desk (help@stsci.edu).
 You may also submit a github issue for either the HSTCAL or WFC3TOOLs repositories.
 
 .. note::
@@ -53,51 +53,45 @@ The :ref:`wf3ccd`, :ref:`wf32d`, :ref:`wf3cte` and :ref:`wf3ir` tasks on the oth
 Running `calwf3` from a python terminal using `wfc3tools`
 ---------------------------------------------------------
 
-In Python without TEAL:
-
 .. code-block:: python
 
     from wfc3tools import calwf3
     calwf3(filename)
 
-In Python with TEAL:
+Parameter Options
+~~~~~~~~~~~~~~~~~
+* input : str or list, default=None
+    Name of input files, such as
+    - a single filename (iaa012wdq_raw.fits)
+    - a Python list of filenames
+    - a partial filename with wildcards (\*raw.fits)
+    - filename of an ASN table (\*asn.fits)
 
-.. code-block:: python
+* output : WHAT IS TYPE, default=None
+    WHAT IS OUTPUT
 
-    from stsci.tools import teal
-    from wfc3tools import calwf3
-    teal.teal('calwf3')
+* printtime : bool, default=False
+    If True, print a detailed time stamp.
 
-Parameter Options
-~~~~~~~~~~~~~~~~~
-* input: str
-    Name of input files
-    * a single filename (iaa012wdq_raw.fits)
-    * a Python list of filenames
-    * a partial filename with wildcards (\*raw.fits)
-    * filename of an ASN table (\*asn.fits)
-* printtime: bool
-    print a detailed time stamp
-* save_tmp: bool
-    save temporary files
-* debug: bool
-    print optionsl debugging statements
-* parallel: bool
-    run the code with OpemMP parallel processing turned on for the UVIS CTE correction
-* log_func: func()
-    if not specified, the print function is used for logging to facilitate use in the Jupyter notebook
-* verbose: bool, optional
-    Print verbose time stamps?
-* quiet: bool, optional
-    Print messages only to trailer file?
-
-
-In Pyraf:
+* save_tmp : bool, default=False
+    If True, save temporary files.
 
-.. code-block:: python
+* verbose : bool, optional, default=False
+    If True, print verbose time stamps.
+
+* debug : bool, default=False
+    If True, print optional debugging statements.
+
+* parallel : bool, default=True
+    If True, run the code with OpemMP parallel processing turned on for the
+    UVIS CTE correction.
+
+* version : bool, default=False
+    If True, WHAT IS VERSION???
 
-    import wfc3tools
-    epar calwf3
+* log_func : func(), default=print()
+    If not specified, the print function is used for logging to facilitate
+    use in the Jupyter notebook.
 
 
 Running many files at the same time
@@ -140,17 +134,17 @@ with an input file and a list of options. This is the same executable that the w
     calwf3.e -vts iaa012wdq_raw.fits
 
 
-    input: str
+    input : str
         Name of input files
             a single filename (``iaa012wdq_raw.fits``)
             the filename of an ASN table (``*_asn.fits``)
 
+        -r : WHATEVER VERSION DOES
         -t : print a detailed time stamp
         -s : save temporary files
+        -v : print verbose time stamps and information
         -d : print optional debugging statements
         -1 : suppress the OpemMP parallel processing for the UVIS CTE correction
-        -v : Print verbose time stamps and information
-        -q : Print messages only to trailer file
 
 
 Running many files at the same time
@@ -170,7 +164,7 @@ Types of files used as input to calwf3
 * _raw file: name of an individual, uncalibrated exposure
 * _crj file: name of any sub-product from an association table
 
-While both CR-SPLIT and REPEAT-OBS exposures from an association get combined using `calwf3`, dithered observations from an association will be combined using `Astrodrizzle <http://www.stsci.edu/hst/HST_overview/drizzlepac/>`_. Images taken at a given dither position can be additionally CR-SPLIT (UVIS only) into multiple exposures.
+While both CR-SPLIT and REPEAT-OBS exposures from an association get combined using `calwf3`, dithered observations from an association will be combined using `Astrodrizzle <https://www.stsci.edu/scientific-community/software/drizzlepac.html>`_. Images taken at a given dither position can be additionally CR-SPLIT (UVIS only) into multiple exposures.
 
 
 When `calwf3` is given an input file, it first discovers which of the above types of files it has provided; a single image, an association table, or a product from an association table. It will then make sure the specified input exists. It then checks to see which DETECTOR the data was observed with and calls the appropriate processing pipeline, either UVIS or IR.
@@ -202,7 +196,7 @@ exposures are combined only with Astrodrizzle, which executes after `calwf3` has
 finished processing all members.
 
 PROD-RPT and PROD-CRJ products are combined useing :ref:`wf3rej` and all output files
-have the cr? extension.
+have the cr extension.
 
 Here's an example of what an association table might contain:
 
@@ -309,13 +303,13 @@ _crc       UVIS calibrated, CR rejected, CTE cleaned image      :math:`e^{-}`
 ========   =================================================    ====================
 
 
-** DRZ and DRC products are produced with Astrodrizzle, see `Astrodrizzle <http://www.stsci.edu/hst/HST_overview/drizzlepac/>`_ **
+** DRZ and DRC products are produced with Astrodrizzle, see `Astrodrizzle <https://www.stsci.edu/scientific-community/software/drizzlepac.html>`_ **
 
 
 Keyword Usage
 -------------
 
-`calwf3` processing is controlled by the values of keywords in the input image headers. Certain keywords, referred to as calibration switches, are used to control which calibration steps are performed. Reference file keywords indicate which reference files to use in the various calibration steps. Users who wish to perform custom reprocessing of their data may change the values of these keywords in the `_raw` FITS file primary headers and then rerun the modified file through  `calwf3`. See the `WFC3 Data Handbook <http://www.stsci.edu/hst/wfc3/documents/handbooks/currentDHB/wfc3_Ch25.html>`_ for a more complete description of these keywords and their values.
+`calwf3` processing is controlled by the values of keywords in the input image headers. Certain keywords, referred to as calibration switches, are used to control which calibration steps are performed. Reference file keywords indicate which reference files to use in the various calibration steps. Users who wish to perform custom reprocessing of their data may change the values of these keywords in the `_raw` FITS file primary headers and then rerun the modified file through  `calwf3`. See the `WFC3 Data Handbook <https://www.stsci.edu/files/live/sites/www/files/home/hst/instrumentation/wfc3/_documents/wfc3_dhb.pdf>`_ for a more complete description of these keywords and their values.
 
 
 Using CRDS to update your reference files

@@ -6,38 +6,38 @@ embedsub
 
 Given an image specified by the user which contains a subarray readout, return a full-frame image with the subarray implanted at the appropriate location.
 
-Usage
-=====
-
-.. code-block:: python
-
-    python
-    from wfc3tools import embedsub
-    embedsub(files)
-
 
 Parameters
 ==========
 
-    files [file]
-        Input image name or list of image names. The rootname will be used to create the output name.
-
+* files : str or list
+    The name of the image file containing the subarray. This can be a
+    single filename or a list of files. The ippsoot will be used to
+    construct the output filename. You should input an FLT image.
 
 
 Returns
 =======
-Return the full-frame location of the subarray coordinates using a  file specified by the user.
+
+* None
+
+
+Usage
+=====
+
+.. code-block:: python
+
+    from wfc3tools import embedsub
+    embedsub(files)
 
 
 Example Output
 ==============
 
 This method calls wfc3tools.sub2full to calculation the subarray position on the full frame image.
 
-This is the default output:
-
-::
+.. code-block:: python
 
-    wfc3tools.embedsub.embedsub('ic5p02eeq_flt.fits')
+    embedsub('ic5p02eeq_flt.fits')
     Subarray image section [x1,x2,y1,y2] = [2828:3339,215:726]
     Image saved to: ic5p02eef_flt.fits
@@ -24,31 +24,6 @@ but you can plot either counts or rate using the optional keyword ``units``.
 .. figure:: ../_static/pstack_example.png
     :align: center
 
-::
-
-    In [1]: xdata,ydata=pstack.pstack('ibh719grq_ima.fits',column=100,row=25,extname='sci')
-
-
-The plotting data is returned as two arrays, to save them into variables issue the command as above:
-
-::
-
-
-    In [1]: xdata
-    Out[2]:
-    array([ 100.651947,   93.470573,   86.2892  ,   79.107826,   71.926453,
-             64.745079,   57.563702,   50.382328,   43.200954,   36.019581,
-             28.838205,   21.65683 ,   14.475455,    7.29408 ,    0.112705,
-              0.      ])
-
-    In [3]: ydata
-    Out[4]:
-    array([ 221.36606389,  219.5396653 ,  182.63100095,  169.178308  ,
-            186.44084352,  158.3105126 ,  129.46997895,  129.92935701,
-            106.14521852,   72.71721539,   69.68652119,   55.98828663,
-             42.30755279,   13.12659422,   27.71404187,    0.        ])
-
-
 
 .. Warning::
     Note that the arrays are structured in SCI order, so the final exposure is the first element in the array
@@ -57,36 +32,73 @@ The plotting data is returned as two arrays, to save them into variables issue t
 Parameters
 ==========
 
-* input [file]
+* filename : str
     Input MultiAccum image name.  This should be either  a  _ima  or _raw  file, containing all the data from multiple readouts.  You must specify just the file name, with no extension designation.
 
-* col [integer]
+* column : int, default=0
     The column index of the pixel to be plotted.
 
-* row [integer]
+* row : int, default=0
     The row index of the pixel to be plotted.
 
-* extname = "sci" [string, allowed values: sci | err | dq | samp | time]
-   Extension name (EXTNAME keyword value) of data to plot.
+* extname : str, default="sci"
+   Extension name (EXTNAME keyword value) of data to plot. Allowed values are "sci", "err", "dq", "samp", and "time".
 
-* units = "counts" [string, allowed values: counts | rate]
-   Plot "sci" or  "err"  data  in  units  of  counts  or  countrate ("rate").   Input data can be in either unit; conversion will be performed automatically.  Ignored when  plotting  "dq",  "samp", or "time" data.
+* units : str, default="counts"
+   Plot "sci" or  "err"  data  in  units  of  counts  or  countrate ("rate").   Input data can be in either unit; conversion will be performed automatically.  Ignored when  plotting  "dq",  "samp", or "time" data. Allowed values are "counts" and "rate".
 
-* title = "" [string]
+* title : str, default=None
    Title  for  the  plot.   If  left  blank,  the name of the input image, appended with  the  extname  and  column  and  row  being plotted, is used.
 
-* xlabel = "" [string]
+* xlabel : str, default=None
    Label  for  the  X-axis  of the plot.  If left blank, a suitable default is generated.
 
-* ylabel = "" [string]
+* ylabel : str, default=None
    Label for the Y-axis of the plot.  If  left  blank,  a  suitable default  based  on the plot units and the extname of the data is generated.
 
-* plot = True [bool]  set plot to false if you only want the data returned
+* plot : bool, default=True
+    If False, return data and do not plot.
+
+Returns
+=======
+
+* xaxis : numpy.ndarray
+   Array of x-axis values that will be plotted.
+
+* yaxis : numpuy.ndarray
+   Array of y-axis values that will be plotted as specified by 'units'.
 
 Usage
 =====
 
 .. code-block:: python
 
     from wfc3tools import pstack
-    xdata,ydata=pstack(inputFilename,column=x,row=y,extname="sci",units="counts|rate",title="",ylabel="",xlabel="")
+    xdata,ydata=pstack(inputFilename,column=x,row=y,extname="sci",units="counts",title="",ylabel="",xlabel="")
+
+Example Output
+==============
+
+::
+
+    In [1]: xdata,ydata=pstack.pstack('ibh719grq_ima.fits',column=100,row=25,extname='sci')
+
+
+The plotting data is returned as two arrays, to save them into variables issue the command as above:
+
+::
+
+
+    In [1]: xdata
+    Out[2]:
+    array([ 100.651947,   93.470573,   86.2892  ,   79.107826,   71.926453,
+             64.745079,   57.563702,   50.382328,   43.200954,   36.019581,
+             28.838205,   21.65683 ,   14.475455,    7.29408 ,    0.112705,
+              0.      ])
+
+    In [3]: ydata
+    Out[4]:
+    array([ 221.36606389,  219.5396653 ,  182.63100095,  169.178308  ,
+            186.44084352,  158.3105126 ,  129.46997895,  129.92935701,
+            106.14521852,   72.71721539,   69.68652119,   55.98828663,
+             42.30755279,   13.12659422,   27.71404187,    0.        ])