Merge pull request #89 from SaraOgaz/tables_doc_addition

some small updates, closes #87

README.rst

@@ -24,5 +24,10 @@ Please open a new `issue <https://github.com/spacetelescope/stak-notebooks/issue
 or new `pull request <https://github.com/spacetelescope/stak-notebooks/pulls>`_
 for bugs, feedback, or new features you would like to see.
 
-If there is an issue you would like to work on, please leave a comment and
-we will be happy to assist. New contributions and contributors are very welcome!
+If there is an issue you would like to work on, please open an issue and
+we will be happy to assist. New contributions and contributors are very welcome! For
+some comprehensive guidlines to contributing on Github, Astropy has a very nice
+write up here: http://docs.astropy.org/en/stable/development/workflow/development_workflow.html.
+But please keep in mind not all repositories on Github will want this contribution workflow.
+If you need some help applying the Astropy contribution guide to this project, we are available for
+questions/guidance.

notebooks/fitsutil.ipynb

@@ -293,10 +293,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 3,
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Astronomy Specific Imports\n",
@@ -305,28 +303,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[3, 4, 7]"
-      ]
-     },
-     "execution_count": 37,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "list=[3,4,5,6,7,7,8]\n",
-    "list[:2]+list[5:6]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -389,7 +366,7 @@
     "\n",
     "# Now save a new copy of the original file without that third extension\n",
     "edited_hdulist = fits.HDUList([hdulist[0],hdulist[1],hdulist[2],hdulist[4],hdulist[5],hdulist[6]])\n",
-    "print(type(edited_hdulist))\n",
+    "print(type(hdulist))\n",
     "print(\"\\n\\nnew FITS file with the 3rd extension taken out:\")\n",
     "edited_hdulist.info()\n",
     "edited_hdulist.writeto(outfile_2, overwrite=True)\n",
@@ -653,7 +630,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.5.4"
   }
  },
  "nbformat": 4,

notebooks/images.imfilter.ipynb

@@ -57,6 +57,9 @@
     "Below we change the matplotlib colormap to ``viridis``.  This is temporarily changing the colormap setting in the matplotlib rc file.\n",
     "\n",
     "\n",
+    "**Important Note to Users:**\n",
+    "There are some differences in algorithms between some of the IRAF and Python Interpolations.  Proceed with care if you are comparing prior IRAF results to Python results.  For more details on this issue see the [filed Github issue](https://github.com/spacetelescope/stak-notebooks/issues/75).\n",
+    "\n",
     "Contents:\n",
     "\n",
     "* [boxcar](#boxcar)\n",

notebooks/images.imgeom.ipynb

@@ -43,6 +43,9 @@
     "\n",
     "The boundary condition options for IRAF and ``scipy`` are the same: nearest, wrap, reflect, and constant.\n",
     "\n",
+    "**Important Note to Users:**\n",
+    "There are some differences in algorithms between some of the IRAF and Python Interpolations.  Proceed with care if you are comparing prior IRAF results to Python results.  For more details on this issue see the [filed Github issue](https://github.com/spacetelescope/stak-notebooks/issues/75).\n",
+    "\n",
     "Contents:\n",
     "\n",
     "* [blkavg](#blkavg)\n",

notebooks/images.imutil.ipynb

@@ -1868,7 +1868,10 @@
    "source": [
     "**Please review the** [Notes](#notes) **section above before running any examples in this notebook**\n",
     "\n",
-    "We will use the ``astropy.stats.sigma_clipped_stats`` function here, which has some wider capabilites then the imstatistics function.  Please see the ``stats`` [package documentation](http://docs.astropy.org/en/stable/api/astropy.stats.sigma_clipped_stats.html) for details on the advanced usage. We also use some Numpy functions for additional statistics."
+    "We will use the ``astropy.stats.sigma_clipped_stats`` function here, which has some wider capabilites then the imstatistics function.  Please see the ``stats`` [package documentation](http://docs.astropy.org/en/stable/api/astropy.stats.sigma_clipped_stats.html) for details on the advanced usage. We also use some Numpy functions for additional statistics.\n",
+    "\n",
+    "**Important Note to Users:**\n",
+    "There are some differences in algorithms between the IRAF and Python statistical calculations.  Proceed with care if you are comparing prior IRAF results to Python results.  For more details on this issue see the [filed Github issue](https://github.com/spacetelescope/stak-notebooks/issues/83)."
    ]
   },
   {

notebooks/tables.ttools.ipynb

@@ -69,7 +69,7 @@
      "data": {
       "text/html": [
        "<i>Table length=5</i>\n",
-       "<table id=\"table90467202944\" class=\"table-striped table-bordered table-condensed\">\n",
+       "<table id=\"table90472151528\" class=\"table-striped table-bordered table-condensed\">\n",
        "<thead><tr><th>sname</th><th>radius</th><th>fwhm</th></tr></thead>\n",
        "<thead><tr><th>str5</th><th>int64</th><th>float64</th></tr></thead>\n",
        "<tr><td>star1</td><td>10</td><td>6.5</td></tr>\n",
@@ -1017,7 +1017,7 @@
    "source": [
     "**Please review the** [Notes](#notes) **section above before running any examples in this notebook**\n",
     "\n",
-    "Tinfo, tlcol and tprint were all used to display information about the table.  Below we show the ``Astropy Table`` equivalents."
+    "Tinfo, tlcol and tprint were all used to display information about the table.  Below we show the ``Astropy Table`` equivalents, including ``showtable`` which is callable from the terminal."
    ]
   },
   {
@@ -1117,6 +1117,97 @@
     "ex_table['sname','fwhm'][0:3]"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[0;31msname radius fwhm\u001b[0m\r\n",
+      "\u001b[0;31m----- ------ ----\u001b[0m\r\n",
+      "star1     10  6.5\r\n",
+      "star2      7  5.1\r\n",
+      "star3      2  0.5\r\n",
+      "star4      1 0.75\r\n",
+      "star5     20 13.0\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "# To print a table outside of a Python interpreter\n",
+    "# Astropy has added the convenience function showtable\n",
+    "!showtable --format ascii /eng/ssb/iraf_transition/test_data/table2.txt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "usage: showtable [-h] [--format FORMAT] [--more] [--info] [--stats]\r\n",
+      "                 [--max-lines MAX_LINES] [--max-width MAX_WIDTH] [--hide-unit]\r\n",
+      "                 [--show-dtype] [--delimiter DELIMITER] [--hdu HDU]\r\n",
+      "                 [--path PATH] [--table-id TABLE_ID]\r\n",
+      "                 filename [filename ...]\r\n",
+      "\r\n",
+      "Print tables from ASCII, FITS, HDF5, VOTable file(s). The tables are read with\r\n",
+      "'astropy.table.Table.read' and are printed with 'astropy.table.Table.pprint'.\r\n",
+      "The default behavior is to make the table output fit onto a single screen\r\n",
+      "page. For a long and wide table this will mean cutting out inner rows and\r\n",
+      "columns. To print **all** the rows or columns use ``--max-lines=-1`` or ``max-\r\n",
+      "width=-1``, respectively. The complete list of supported formats can be found\r\n",
+      "at http://astropy.readthedocs.io/en/latest/io/unified.html#built-in-table-\r\n",
+      "readers-writers\r\n",
+      "\r\n",
+      "positional arguments:\r\n",
+      "  filename              path to one or more files\r\n",
+      "\r\n",
+      "optional arguments:\r\n",
+      "  -h, --help            show this help message and exit\r\n",
+      "  --format FORMAT       input table format, should be specified if it cannot\r\n",
+      "                        be automatically detected\r\n",
+      "  --more                use the pager mode from Table.more\r\n",
+      "  --info                show information about the table columns\r\n",
+      "  --stats               show statistics about the table columns\r\n",
+      "\r\n",
+      "pprint arguments:\r\n",
+      "  --max-lines MAX_LINES\r\n",
+      "                        maximum number of lines in table output\r\n",
+      "                        (default=screen length, -1 for no limit)\r\n",
+      "  --max-width MAX_WIDTH\r\n",
+      "                        maximum width in table output (default=screen width,\r\n",
+      "                        -1 for no limit)\r\n",
+      "  --hide-unit           hide the header row for unit (which is shown only if\r\n",
+      "                        one or more columns has a unit)\r\n",
+      "  --show-dtype          include a header row for column dtypes\r\n",
+      "\r\n",
+      "ASCII arguments:\r\n",
+      "  --delimiter DELIMITER\r\n",
+      "                        column delimiter string\r\n",
+      "\r\n",
+      "FITS arguments:\r\n",
+      "  --hdu HDU             name of the HDU to show\r\n",
+      "\r\n",
+      "HDF5 arguments:\r\n",
+      "  --path PATH           the path from which to read the table\r\n",
+      "\r\n",
+      "VOTable arguments:\r\n",
+      "  --table-id TABLE_ID   the table to read in\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Here is the showtable help for more details on usage\n",
+    "!showtable --help"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1545,12 +1636,12 @@
    "source": [
     "**Please review the** [Notes](#notes) **section above before running any examples in this notebook**\n",
     "\n",
-    "Tselect is used to create a new table from selected rows, tproject from selected columns, and tquery from a combination of selected rows and columns.  We show two examples of how to generate a new table from selected columns and selected rows.  You can combine these two pieces of code in either order to get a tquery like result.  There is an alternate way to do selections if you have already organized your table into groups by using the [filter method](http://docs.astropy.org/en/stable/table/operations.html#filtering), but the user will still need to write a custom filtering function to provide to ``filter``."
+    "Tselect is used to create a new table from selected rows, tproject from selected columns, and tquery from a combination of selected rows and columns.  We show two examples of how to generate a new table from selected columns and selected rows.  You can combine these two pieces of code in either order to get a tquery like result. For row filtering we combine boolean masks using the [Python bitwise operators](https://docs.python.org/3.5/library/stdtypes.html#bitwise-operations-on-integer-types). There is an alternate way to do selections if you have already organized your table into groups by using the [filter method](http://docs.astropy.org/en/stable/table/operations.html#filtering), but the user will still need to write a custom filtering function to provide to ``filter``."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 35,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1560,7 +1651,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [
     {
@@ -1570,23 +1661,23 @@
       "sname radius fwhm\n",
       "----- ------ ----\n",
       "star4      1 0.75\n",
-      "star5     20  4.5\n"
+      "star5     20 13.0\n"
      ]
     }
    ],
    "source": [
-    "# For selecting rows we give the new table an initial column setup, \n",
-    "# copied from the original table through the dtype keyword\n",
+    "# For selecting rows can use bitwise operators to generate a boolean mask\n",
     "table1 = Table(dtype=ex_table.dtype)\n",
-    "for row in ex_table:\n",
-    "    if row['sname'] == 'star4' or row['radius'] == 20:\n",
-    "        table1.add_row(row)\n",
-    "table1.pprint()"
+    "boolean_mask = (ex_table['sname'] == 'star4') | (ex_table['radius'] == 20)\n",
+    "\n",
+    "# \n",
+    "subset = ex_table[boolean_mask]\n",
+    "subset.pprint()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [
     {
@@ -1599,16 +1690,14 @@
       "star2  5.1\n",
       "star3  0.5\n",
       "star4 0.75\n",
-      "star5  4.5\n"
+      "star5 13.0\n"
      ]
     }
    ],
    "source": [
-    "# For selecting columns we start with an empty new table\n",
-    "table2 = Table()\n",
-    "for col in ex_table.itercols():\n",
-    "    if col.name in ['sname','fwhm']:\n",
-    "        table2[col.name] = col\n",
+    "# For selecting columns we can pull the required columns \n",
+    "# out of the original table with the column names\n",
+    "table2 = ex_table['sname','fwhm']\n",
     "table2.pprint()"
    ]
   },