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minor doc update for calwf3v3.4 delivery
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sosey committed Sep 26, 2016
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4 changes: 2 additions & 2 deletions docs/wfc3tools/calwf3.rst
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Expand Up @@ -16,7 +16,7 @@ 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 is also installed along with the STScI distributed package `Astroconda <http://astroconda.readthedocs.io/en/latest/installation.html>`_ .


A detailed description of the improved `calwf3`, Version 3.3, which is more generally referred to as the UVIS2.0 update, will be available in a future publication of WFC3 Data Handbook and several ISRs which will accompany the update.
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>`_.

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).
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Displaying output from calwf3 in a Jupyter Notebook
---------------------------------------------------

When calling `calwf3` from a Jupyter notebook or from the python wrappers, informational text output from the underlying `calwf3.e` program will be passed through `print as the calibration runs by default, and show up in the user's cell. This behavior can be customized by passing your own function as the `log_func` keyword argument to `calwf3`. As output is read from the underlying program, the `calwf3` Python wrapper will call `log_func` with the contents of each line. (`print` is an obvious choice for a log function, but this also provides a way to connect `calwf3` to the Python logging system by passing the `logging.debug function or similar.)
When calling `calwf3` from a Jupyter notebook or from the python wrappers, informational text output from the underlying `calwf3.e` program will be passed through `print as the calibration runs by default, and show up in the user's cell. This behavior can be customized by passing your own function as the `log_func` keyword argument to `calwf3`. As output is read from the underlying program, the `calwf3` Python wrapper will call `log_func` with the contents of each line. (`print` is an obvious choice for a log function, but this also provides a way to connect `calwf3` to the Python logging system by passing the `logging.debug` function or similar.)

If log_func=None` is passed, informational text output from the underlying program will be ignored, but the program's exit code will still be checked for successful completion.

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3 changes: 3 additions & 0 deletions docs/wfc3tools/history.rst
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Expand Up @@ -7,6 +7,9 @@ Software Update History for HSTCAL.CALWF3

.. warning:: IRAF version of WFC3 no longer maintained or delivered, use WFC3TOOLS in HSTCAL or call the executable from your operating system command line. With version 3.3 the pipeline now produces two versions of each calibrated file, one set with the CTE correction applied and one set without the CTE correction applied

**Updates for Version 3.4 26-Sep-2016 MLS**
- Fixed memory allocation around some print statements

**Updates for Version 3.4 20-Sep-2016 MLS**
- Moved the init for the CTE params back to the top of the code, it had gotten moved below the header update for the information

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2 changes: 1 addition & 1 deletion docs/wfc3tools/ir_pipeline.inc
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Expand Up @@ -176,7 +176,7 @@ This step fits the accumulating signal up the image ramp and identifies cosmic-r

.. note::

With the release of `calwf3` version 3.3, the WFC3 Science Team requested that HST Data Processing also change the way IR SCAN data was processed in the pipeline. Specifically, that data processing set the value of CRCORR to OMIT. CALWF3 performs up-the-ramp fitting during the CRCORR step, which for scan data produces a minimally useful result. Setting CRCORR=OMIT stops the ramp fit from happening and instead produces an FLT output image which contains the first-minus-last read result. This by nature is not a count-rate image, but a count image if UNITCORR = OMIT. UNITCORR converts the image to count rates. Additionally, if FLATCORR is set to complete then the output units should be in electrons, otherwise they are in counts.
With the release of `calwf3 v3.3`, the WFC3 Science Team requested that HST Data Processing also change the way IR SCAN data was processed in the pipeline. Specifically, that data processing set the value of CRCORR to OMIT. CALWF3 performs up-the-ramp fitting during the CRCORR step, which for scan data produces a minimally useful result. Setting CRCORR=OMIT stops the ramp fit from happening and instead produces an FLT output image which contains the first-minus-last read result. This by nature is not a count-rate image, but a count image if UNITCORR = OMIT. UNITCORR converts the image to count rates. Additionally, if FLATCORR is set to complete then the output units should be in electrons, otherwise they are in counts.



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4 changes: 2 additions & 2 deletions docs/wfc3tools/uvis_pipeline.inc
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Expand Up @@ -13,7 +13,7 @@ UVIS Pipleline

Flow diagram for ``calwf3`` data. :ref:`wf3cte` occurs as the very first step, before :ref:`wf3ccd`.

As of version 3.3, the calwf3 pipeline processes all UVIS data twice, once with the CTE correction applied as the first step, and a second time without the CTE correction. A short description of the calibration steps, in the order they are performed:
As of `calwf3 v3.3`, the calwf3 pipeline processes all UVIS data twice, once with the CTE correction applied as the first step, and a second time without the CTE correction. A short description of the calibration steps, in the order they are performed:

* Calculate and remove and CTE found in the image (PCTECORR)
* Calculate a noise model for each pixel and record in the error array (ERR) of the image (NOISCORR)
Expand Down Expand Up @@ -94,7 +94,7 @@ Flagging of SINK pixels in the DQ extension of calibrated images is controlled w
`WFC3 ISR 2014-19 <http://www.stsci.edu/hst/wfc3/documents/ISRs/WFC3-2014-19.pdf>`_ has a detailed analysis on detection of the sink pixels, while the strategy for flagging them is discussed in `WFC3 ISR 2014-22 <http://www.stsci.edu/hst/wfc3/documents/ISRs/WFC3-2014-22.pdf>`_ .
Sink pixels are currently only flagged in full frame science images, a future release of `calwf3` will also perform flagging in subarray images.
Sink pixels are currently only flagged in full frame science images, `calwf3v3.4` will also perform flagging in subarray images.
**The pipeline currently does no further analysis or correction on pixels which have been flagged as affected by sink pixels**
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2 changes: 1 addition & 1 deletion docs/wfc3tools/wf3rej.rst
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Expand Up @@ -32,7 +32,7 @@ Displaying output from wf3rej in a Jupyter Notebook

When calling `wf3rej` from a Jupyter notebook, informational text output from the underlying `wf3rej.e` program will be passed through `print` as the calibration runs by default, and show up in the user's cell. This behavior can be customized by passing your own function as the `log_func` keyword argument to `wf3rej`. As output is read from the underlying program, the `wf3rej` Python wrapper will call `log_func` with the contents of each line. (`print` is an obvious choice for a log function, but this also provides a way to connect `wf3rej` to the Python logging system by passing the logging.debug` function or similar.)

If `log_func=None is passed, informational text output from the underlying program will be ignored, but the program's exit code will still be checked for successful completion.
If `log_func=None` is passed, informational text output from the underlying program will be ignored, but the program's exit code will still be checked for successful completion.



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