STScI_Python Version 2.12 Release Notes
August 2011
This release includes new versions of PyRAF, PyFITS, STWCS, pytools,
Multidrizzle, and related tasks. This release also includes
instrument-specific packages to support ACS, NICMOS, and COS.
The convolve, image, and ndimage packages have been included with
this release to insure compatibility with the rest of our code.
Platform Support
================
Normally, platform support issues do not apply to Python tasks,
as most Python code will run on all platforms on which Python has
been installed. This distribution was tested to correctly support
installation on Linux and Mac OS X 10.6 (Snow Leopard), while an
installation for Windows will be provided at a later date. As of the
June 2010 release, PyRAF no longer requires the installation of IRAF.
Note that the only IRAF distribution for Windows runs under Cygwin,
but no testing of PyRAF has been conducted under Cygwin.
No Solaris Support
------------------
This release has NOT been tested on the Solaris platform. We no longer
build Solaris binaries for STSDAS, although the source code can always
be downloaded and compiled locally as needed.
Documentation
=============
Documentation for these tasks has been consolidated into a
single location complete with an index viewable as a local web
page. The documentation includes any available user guides and
API documentation generated using 'EPYDOC' for the modules or
packages. This index can be accessed using:
--> import stscidocs
--> stscidocs.viewdocs()
--> stscidocs.help()
This will automatically bring up the default web browser application
to display the index page. All the available documentation for
software packaged with this distribution can be accessed through this
interface, as this documentation resides locally upon installation.
Python Environment
==================
This release has been tested using Python Versions 2.5.4 and 2.7. This
release also requires at least numpy 1.3. All packages within this
release have been revised to support easy_install of the code, while
still allowing the code to be installed using the disutils command
'python setup.py'.
Namespace Changes
==================
The organization of the stsci_python package has been significantly
changed to move many packages into the 'stsci' namespace and remove
any package name confusion (such as 'pytools' which is used as a name
by other Python software). The namespace changes require dependent
packages to update to point to the new names of the packages based
on this translation table:
old name ---> new name
---------- -------------
convolve stsci.convolve
image stsci.image
imagemanip stsci.imagemanip
imagestats stsci.imagestats
numdisplay stsci.numdisplay
pytools stsci.tools
stimage stsci.stimage
ndimage stsci.ndimage
The 'ndimage', 'image', and 'convolve' packages included in our release
are forked from SciPy in order to support our software needs without
requiring all of SciPy to be installed separately.
PyFITS Version 3.0.0
====================
This release now includes and relies on PyFITS 3.0.0, a version which
contains changes to interfaces that are incompatible with previous
versions of PyFITS. These changes were implemented to allow PyFITS to
be translated to work with Python 3.0 while refactoring the code to make
it easier to maintain.
The PyFITS Release Notes (and file 'CHANGES.txt' included in the release)
contain detailed descriptions of all the changes made to PyFITS 3.0.0.
The code in this release has been modified to be compatible with both
PyFITS 3.0.0 and earlier versions of PyFITS, however, this compatibility
will be removed at some point in the future.
This release addresses an extensive list of bug fixes and improvements,
including:
- Calls to deprecated functions will display a Deprecation warning. However,
in Python 2.7 and up Deprecation warnings are ignored by default, so run
Python with the `-Wd` option to see if you're using any deprecated
functions. If we get close to actually removing any functions, we might
make the Deprecation warnings display by default.
- Added basic Python 3 support
- Added support for multi-dimensional columns in tables as specified by the
TDIMn keywords (#47)
- Fixed a major memory leak that occurred when creating new tables
with the `new_table()` function (where strings are padded with
zero-bytes) vs ASCII tables (where strings are padded with spaces)
- Fixed a bug in which the case of Random Access Group parameters names
was not preserved when writing
- Added support for binary table fields with zero width
- Added support for wider integer types in ASCII tables; although this
is non- standard, some GEIS images require it
- Fixed a bug that caused the index_of() method of HDULists to crash
when the HDUList object is created from scratch
- Fixed the behavior of string padding in binary tables (where strings
should be padded with nulls instead of spaces)
- Fixed a rare issue that caused excessive memory usage when computing
checksums using a non-standard block size
- Add support for forced uint data in image sections
- Fixed tuple and list-based indexing of FITS_rec objects
- Fixed an issue where BZERO and BSCALE keywords were appended to
headers in the wrong location
- `FITS_record` objects (table rows) have full slicing support, including
stepping, etc.
- Fixed a bug where updating multiple files simultaneously (such as when
running parallel processes) could lead to a race condition with mktemp()
- Fixed a bug where compressed image headers were not in the order
expected by the funpack utility
stsci.tools (formerly: pytools)
============
This package provides utilities which support multiple packages due
to the more general nature. Updates include:
- New modules were added to work with GEIS (IRAF) images:
specifically, the 'swapgeis' module to byteswap a GEIS image
and the 'convertgeis' to replace the 'stwfits' task in IRAF to
write out a waivered-FITS image from a GEIS image.
- Removed the use of 'numerixenv' so that code will now only
support numpy.
- Updated the 'buildRootname()' function in 'tools.fileutil'
to retain and properly handle any paths provided for the input
filename
- There were many improvements to the TEAL parameter interface:
- TEAL now handles .cfgspc changes/upgrades with a notice
stating which parameters are "problems" in the changed
version (#728, r11322, PyRAF ticket #127).
- Changes were made to the TEAL code to prepare for the port
to Python 3 (#584), although Python 2.x will be supported
for quite some time. TEAL does now run under Python 3
(via 2to3), but this has not yet been heavily tested
(expected next release).
- TEAL is now smarter about showing task help in HTML where
possible, and it also has hooks to jump to parameter-specific
help topics (#614, r12000, r12863)
- Some GUI items were fixed: font colors, Save-As dialog,
a FileDialog which changes directory when it shouldn't
(#727, r12344, r12462, r12995).
- Parameter mismatch errors are now more easy to
read/understand.
- TEAL supports two new trigger keywords: "set_yes_if" and
"set_no_if". Set the env. variable TEAL_DEBUG to have TEAL
print out trigger logic (#725).
calcos
============
Version 2.14.4 was previously released as a patch in April. This
release includes CALCOS Version 2.15.4 with updates from 2.14.4
that include:
- A 'walk' correction was added to CALCOS to correct the pixel
coordinates of events in an FUV TIME-TAG exposure for shifts
which are dependent on the pulse height amplitude (PHA).
- Use exposure appropriate for each FUV data segment in the
x1d correction.
- A bug in background smoothing during spectral extraction has
been fixed. This mostly affects values near the endpoints of
the spectrum.
In this release, there is an unexplained problem on Windows; CALCOS
cannot be imported.
costools
============
A new package containing COS-specific analysis tasks has been added to
this release. Currently, the only task included in this new package
is the 'timefilter' task. This program reads a COS corrtag file and
sets flags in the DQ column of the EVENTS extension depending on the
filter that was specified.
imagestats (now: stsci.imagestats)
============
The imagestats package was updated to take into account any
user-specified limits when clipping has been requested so that it
behaves more like IRAF's imagestats task.
numdisplay (now: stsci.numdisplay)
============
Numdisplay version 1.6.1 corrects a problem with compatibility with
numpy versions > 2.0. This version has been tested to work under
Python 2.7 using all the latest versions of numpy.
pydrizzle
============
Only minor changes were made to allow this version to work with PyFITS 3.0.0.
PyRAF v1.11
============
This release supports Python 2.5, 2.6, and 2.7. Since the 1.10 bundled release, the following enhancements have been made:
- PyRAF is being prepared for the port to Python 3. Many code changes
were made, though there should be no behavior changes noticeable
to the user (#137, #154).
- PyRAF was modified to maintain compatibility with IRAF 2.15.*,
both 32 and 64-bit (mostly due to graphics WCS changes). Also,
better error messaging was implemented within PyRAF's core in
order to debug related problems, often seen during startup. See
PyRAF FAQ #1.5 (#156 and r1324).
- PyRAF is now more robust in the face of outdated or changing CL
scripts, e.g. login.cl. The ErrorTracker class, used internally, is
now keeping better track of offensive CL script code for reporting
to the user.
- The 'unlearn' command is now available for TEAL-enabled tasks
(r1412,3). TEAL also now automatically switches focus like EPAR
(#159).
- PyRAF on Windows now has a desktop icon for launching the
command-line interface (#130).
and the following bugs have been fixed:
- EPAR for TEAL-enabled tasks (.cfg file) now more elegantly handles
changes to that task's .cfgspc definition: no traceback, simpler
error message or, in some cases, even a dialog (#127). Validation
errors are also handled more gracefully now (#158).
- It was noticed that text-based help in the terminal would not run
without graphics capabilities, even though it should not require
them (#147).
- On OSX, Python itself will no longer crash in a remote session if
aqutil fails to load (#149).
- A bug in the Page menu (graphics windows) was fixed for the
matplotlib graphics kernel (#150). Also fixed in this graphics
kernel was redraws not occurring with 't' during implot (r1387).
- CL script parsing is now catching cases where a "#" is found in
the right hand side of a set/reset statement (#155).
- Integer division was not behaving correctly in parsed CL code. See
PyRAF FAQ #6.6 for a full discussion of the expected behavior
(#157).
- PyRAF was throwing a traceback during a warning about certain CL
system/shell commands (#162).
- PyRAF on Windows no longer requires the use of the HOME environment
variable (#130).
Python 3 Note: It is anticipated that the next full release of PyRAF
(late 2011/early 2012) will have basic capabilities working under
Python 3. Python 2.x however will be supported for quite a while. Many
users will be cautious about converting their scripts and processing.
pysynphot
============
The following changes have been made since the 0.8.2 release:
Bugfixes
---------
- Calculation of the pivot wavelength is now correctly implemented
as a method (.pivot) on Bandpass objects.
- The GaussianSource, Powerlaw, FlatSpectrum, and BlackBody classes
have been fixed so that they are consistent after unit changes
using the convert() method.
- Fixed multiple bugs in the InterpolatedSpectralElement class so that
it correctly handles tables with different column designs and
provides correctly interpolated results for all table input
types. (Previously, interpolation was implemented correctly only
for ramp filters.)
- Handling of MergedWavesets was corrected to strictly eliminate
duplicate entries, which previously sometimes occurred due to
numerical rounding during merge operations.
Performance
-----------
- Calculating binned flux for Observation objects has been moved to
an optional C extension to improve speed. If the C extension is not
available at run time,
the calculations are performed in Python.
- Objects created when opening and reading tables are cached to
improve speed
in situations where a table previously would have been opened and
closed many times within a program.
Other changes
-------------
- Custom pysynphot exceptions have been implemented for some conditions
that previously raised ValueErrors. Additional custom exceptions
will be implemented in the next release.
- The CompTable and GraphTable classes have been moved to a new
pysynphot module called tables.
- The etc module has been deprecated. The etc.parse_spec function
has been relocated to spparser.parse_spec.
stwcs
============
The package has been updated with these changes:
- added logging to STWCS
- added support for a WCSCORR table which summarizes all updates
made to the WCS information of each SCI extension
- The HSTWCS method 'wcs2header' was modified to correctly append
the SIP and IDC distortion model keywords to the header
- The logic for using the 'readModel()' method of HSTWCS was
also improved to not try and read the IDCModel when no 'idctab'
had been specified in the header.
- eliminated the 1 pixel offset introduced when creating an output
WCS with an input WCS which has no distortion model.
- makes recognition of non-HST data (slightly) more general so
that it will work on data created with IRAF's artdata package
- added 'all_sky2pix()' method to HSTWCS objects which implements
an iterative solution using the full distortion model to convert
sky positions into pixel positions
- Added a tool to create a virtual mosaic based on the WCS of the
input observations, with the option to provide an output tangent
plane for the virtual mosaic
- Added a method to update the scale of a WCS object:
updatePscale()
