[yt-svn] commit/yt-doc: 9 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri Nov 22 13:26:36 PST 2013
9 new commits in yt-doc:
https://bitbucket.org/yt_analysis/yt-doc/commits/68c1428a892b/
Changeset: 68c1428a892b
User: chummels
Date: 2013-11-22 21:39:07
Summary: Adding section to examining docs on how to use covering grids to inspect data.
Affected #: 1 file
diff -r 22ed952097eae7a815469260e97f7d25cfd85767 -r 68c1428a892be0d91497f1eebcb464089ecd7aa1 source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -115,3 +115,95 @@
Note that this doesn't just return the canonical output, but also all of the
parent grids that overlap with that point.
+
+
+Examining Data in a Fixed Resolution Array
+----------------------------~~~~~~~~~~~~~~
+
+If you have a dataset, either AMR or single resolution, and you want to just
+stick it into a fixed resolution numpy array for later examination, then you
+want to use a :ref:`Covering Grid <available-objects>`. You must specify the
+maximum level at which to sample the data, a left edge of the data where you
+will start, and the resolution at which you want to sample.
+
+For example, let's use the :ref:`sample dataset <getting-sample-data>`
+``Enzo_64``. This dataset is at a resolution of 64^3 with 5 levels of AMR,
+so if we want a 64^3 array covering the entire volume and sampling just the
+lowest level data, we run:
+
+.. code-block:: python
+
+ from yt.mods import *
+ pf = load('Enzo_64/DD0043/data0043')
+ all_data_level_0 = pf.h.covering_grid(level=0, left_edge=[0,0.0,0.0],
+ dims=[64, 64, 64])
+
+Note that we can also get the same result and rely on the dataset to know
+its own underlying dimensions:
+
+.. code-block:: python
+
+ all_data_level_0 = pf.h.covering_grid(level=0, left_edge=[0,0.0,0.0],
+ dims=pf.domain_dimensions)
+
+We can now access our underlying data at the lowest level by specifying what
+:ref:`field <field-list>` we want to examine:
+
+.. code-block:: python
+ print all_data_level_0['Density'].shape
+ (64, 64, 64)
+
+ print all_data_level_0['Density']
+
+ array([[[ 1.92588925e-31, 1.74647692e-31, 2.54787518e-31, ...,
+
+ print all_data_level_0['Temperature'].shape
+ (64, 64, 64)
+
+If you create a covering grid that spans two child grids of a single parent
+grid, it will fill those zones covered by a zone of a child grid with the
+data from that child grid. Where it is covered only by the parent grid, the
+cells from the parent grid will be duplicated (appropriately) to fill the
+covering grid.
+
+Let's say we now want to look at that entire data volume and sample it at the
+a higher resolution (i.e. level 2). As stated above, we'll be oversampling
+under-refined regions, but that's OK. We must also increase the resolution
+of our output array by a factor of 2^2 in each direction to hold this new
+larger dataset:
+
+.. code-block:: python
+
+ all_data_level_2 = pf.h.covering_grid(level=2, left_edge=[0,0.0,0.0],
+ dims=pf.domain_dimensions * 2**2)
+
+And let's see what's the density in the central location:
+
+.. code-block:: python
+
+ print all_data_level_2['Density'].shape
+ (256, 256, 256)
+
+ print all_data_level_2['Density'][128, 128, 128]
+ 1.7747457571203124e-31
+
+There are two different types of covering grids: unsmoothed and smoothed.
+Smoothed grids will be filled through a cascading interpolation process;
+they will be filled at level 0, interpolated to level 1, filled at level 1,
+interpolated to level 2, filled at level 2, etc. This will help to reduce
+edge effects. Unsmoothed covering grids will not be interpolated, but rather
+values will be duplicated multiple times.
+
+To sample our dataset from above with a smoothed covering grid in order
+to reduce edge effects, it is a nearly identical process:
+
+.. code-block:: python
+
+ all_data_level_2_s = pf.h.smoothed_covering_grid(2, [0.0, 0.0, 0.0],
+ pf.domain_dimensions * 2**2)
+
+ print all_data_level_2_s['Density'].shape
+ (256, 256, 256)
+
+ print all_data_level_2_s['Density'][128, 128, 128]
+ 1.763744852165591e-31
https://bitbucket.org/yt_analysis/yt-doc/commits/39fa95987393/
Changeset: 39fa95987393
User: chummels
Date: 2013-11-22 21:40:54
Summary: Adding sphinx tags to examining section.
Affected #: 1 file
diff -r 68c1428a892be0d91497f1eebcb464089ecd7aa1 -r 39fa9598739382ff1d91e1b7c7fbacc08829428e source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -1,3 +1,5 @@
+.. _low-level-data-inspection:
+
Low-Level Data Inspection
=========================
@@ -13,6 +15,8 @@
For a more basic introduction, see :ref:`bootcamp` and more specifically
:ref:`data_inspection`.
+.. _examining-grid-hierarchies:
+
Examining Grid Hierarchies
--------------------------
@@ -64,6 +68,8 @@
g2 = g.Children[1].Children[0]
print g2.LeftEdge
+.. _examining-grid-data:
+
Examining Grid Data
-------------------
@@ -92,6 +98,8 @@
This field will be the raw data found in the file.
+.. _finding-data-at-fixed-points:
+
Finding Data at Fixed Points
----------------------------
@@ -116,6 +124,7 @@
Note that this doesn't just return the canonical output, but also all of the
parent grids that overlap with that point.
+.. _examining-data-in-a-fixed-resolution-array:
Examining Data in a Fixed Resolution Array
----------------------------~~~~~~~~~~~~~~
https://bitbucket.org/yt_analysis/yt-doc/commits/a98cabf73fa8/
Changeset: a98cabf73fa8
User: chummels
Date: 2013-11-22 21:47:23
Summary: adding section to examining docs introducing FRB and linking to full FRB section in manual plotting interface docs.
Affected #: 1 file
diff -r 39fa9598739382ff1d91e1b7c7fbacc08829428e -r a98cabf73fa8a5fe4b15c659f7f8dec9d4adf315 source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -127,7 +127,7 @@
.. _examining-data-in-a-fixed-resolution-array:
Examining Data in a Fixed Resolution Array
-----------------------------~~~~~~~~~~~~~~
+------------------------------------------
If you have a dataset, either AMR or single resolution, and you want to just
stick it into a fixed resolution numpy array for later examination, then you
@@ -216,3 +216,19 @@
print all_data_level_2_s['Density'][128, 128, 128]
1.763744852165591e-31
+
+.. _examining-image-data-in-a-fixed-resolution-array:
+
+Examining Image Data in a Fixed Resolution Array
+------------------------------------------------
+
+In the same way that one can sample a multi-resolution 3D dataset by placing
+it into a fixed resolution 3D array as a
+:ref:`Covering Grid <examining-data-in-a-fixed-resolution-array>`, one can
+also access the raw image data that is returned from various yt functions
+directly as a fixed resolution array. This provides a means for bypassing the
+yt method for generating plots, and allows the user the freedom to use
+whatever interface they wish for displaying and saving their image data.
+The object for doing this is the aptly titled Fixed Resolution Buffer, and
+there is a full explanation for how to use it
+:ref:`here <slice-projections-and-other-images-the-fixed-resolution-buffer>`.
https://bitbucket.org/yt_analysis/yt-doc/commits/96f09a0b7938/
Changeset: 96f09a0b7938
User: chummels
Date: 2013-11-22 21:54:41
Summary: Fixing broken link in low-level data examination.
Affected #: 1 file
diff -r a98cabf73fa8a5fe4b15c659f7f8dec9d4adf315 -r 96f09a0b7938b7cc8b61fc82d07c6e25b4eb3bff source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -231,4 +231,4 @@
whatever interface they wish for displaying and saving their image data.
The object for doing this is the aptly titled Fixed Resolution Buffer, and
there is a full explanation for how to use it
-:ref:`here <slice-projections-and-other-images-the-fixed-resolution-buffer>`.
+:ref:`here <fixed-resolution-buffers>`.
https://bitbucket.org/yt_analysis/yt-doc/commits/e9bf5d2d2a78/
Changeset: e9bf5d2d2a78
User: chummels
Date: 2013-11-22 21:55:58
Summary: Changing subtitle to be more descriptive of covering grid.
Affected #: 1 file
diff -r 96f09a0b7938b7cc8b61fc82d07c6e25b4eb3bff -r e9bf5d2d2a781ce8fee625accba98aaf63a05d32 source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -124,10 +124,10 @@
Note that this doesn't just return the canonical output, but also all of the
parent grids that overlap with that point.
-.. _examining-data-in-a-fixed-resolution-array:
+.. _examining-grid-data-in-a-fixed-resolution-array:
-Examining Data in a Fixed Resolution Array
-------------------------------------------
+Examining Grid Data in a Fixed Resolution Array
+-----------------------------------------------
If you have a dataset, either AMR or single resolution, and you want to just
stick it into a fixed resolution numpy array for later examination, then you
@@ -224,7 +224,7 @@
In the same way that one can sample a multi-resolution 3D dataset by placing
it into a fixed resolution 3D array as a
-:ref:`Covering Grid <examining-data-in-a-fixed-resolution-array>`, one can
+:ref:`Covering Grid <examining-grid-data-in-a-fixed-resolution-array>`, one can
also access the raw image data that is returned from various yt functions
directly as a fixed resolution array. This provides a means for bypassing the
yt method for generating plots, and allows the user the freedom to use
https://bitbucket.org/yt_analysis/yt-doc/commits/93c4c6829793/
Changeset: 93c4c6829793
User: chummels
Date: 2013-11-22 21:56:55
Summary: Merged yt_analysis/yt-doc into default
Affected #: 2 files
diff -r e9bf5d2d2a781ce8fee625accba98aaf63a05d32 -r 93c4c6829793bd0eb9110414c7af8aca12a3e10d source/examining/Loading_Generic_Array_Data.ipynb
--- a/source/examining/Loading_Generic_Array_Data.ipynb
+++ b/source/examining/Loading_Generic_Array_Data.ipynb
@@ -271,6 +271,108 @@
"level": 3,
"metadata": {},
"source": [
+ "Volume Rendering Loaded Data"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Volume rendering requires defining a `TransferFunction` to map data to color and opacity and a `camera` to create a viewport and render the image."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "#Find the min and max of the field\n",
+ "mi, ma = pf.h.all_data().quantities[\"Extrema\"]('Temperature')[0]\n",
+ "#Reduce the dynamic range\n",
+ "mi += 1.5e7\n",
+ "ma -= 0.81e7"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Create a Transfer Function that goes from the minimum to the maximum of the data:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "tf = ColorTransferFunction((mi, ma), grey_opacity=False)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Define the properties and size of the `camera` viewport:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Choose a vector representing the viewing direction.\n",
+ "L = [0.5, 0.5, 0.5]\n",
+ "# Define the center of the camera to be the domain center\n",
+ "c = pf.domain_center\n",
+ "# Define the width of the image\n",
+ "W = 1.5*pf.domain_width\n",
+ "# Define the number of pixels to render\n",
+ "Npixels = 512 "
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Create a `camera` object and "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "cam = pf.h.camera(c, L, W, Npixels, tf, fields=['Temperature'],\n",
+ " north_vector=[0,0,1], steady_north=True, \n",
+ " sub_samples=5, no_ghost=False,log_fields=False)\n",
+ "\n",
+ "cam.transfer_function.map_to_colormap(mi,ma, \n",
+ " scale=15.0, colormap='algae')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "cam.show()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "heading",
+ "level": 3,
+ "metadata": {},
+ "source": [
"FITS image data"
]
},
diff -r e9bf5d2d2a781ce8fee625accba98aaf63a05d32 -r 93c4c6829793bd0eb9110414c7af8aca12a3e10d source/visualizing/volume_rendering.rst
--- a/source/visualizing/volume_rendering.rst
+++ b/source/visualizing/volume_rendering.rst
@@ -256,10 +256,10 @@
.. _transfer-function-helper:
-TransferFunctionHelpler
------------------------
+TransferFunctionHelper
+----------------------
-.. notebook:: TransferFunctionHelpler_Tutorial.ipynb
+.. notebook:: TransferFunctionHelper_Tutorial.ipynb
.. _healpix_volume_rendering:
https://bitbucket.org/yt_analysis/yt-doc/commits/b3f928d031cf/
Changeset: b3f928d031cf
User: chummels
Date: 2013-11-22 22:18:43
Summary: Fixing sphinx error.
Affected #: 1 file
diff -r e9bf5d2d2a781ce8fee625accba98aaf63a05d32 -r b3f928d031cf9d99317a1aee85c6ee051d0c5c96 source/examining/low_level_inspection.rst
--- a/source/examining/low_level_inspection.rst
+++ b/source/examining/low_level_inspection.rst
@@ -159,6 +159,7 @@
:ref:`field <field-list>` we want to examine:
.. code-block:: python
+
print all_data_level_0['Density'].shape
(64, 64, 64)
https://bitbucket.org/yt_analysis/yt-doc/commits/62499b35280b/
Changeset: 62499b35280b
User: chummels
Date: 2013-11-22 22:19:14
Summary: Merging.
Affected #: 2 files
diff -r b3f928d031cf9d99317a1aee85c6ee051d0c5c96 -r 62499b35280bf517006308094385fa7f7a946c85 source/examining/Loading_Generic_Array_Data.ipynb
--- a/source/examining/Loading_Generic_Array_Data.ipynb
+++ b/source/examining/Loading_Generic_Array_Data.ipynb
@@ -271,6 +271,108 @@
"level": 3,
"metadata": {},
"source": [
+ "Volume Rendering Loaded Data"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Volume rendering requires defining a `TransferFunction` to map data to color and opacity and a `camera` to create a viewport and render the image."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "#Find the min and max of the field\n",
+ "mi, ma = pf.h.all_data().quantities[\"Extrema\"]('Temperature')[0]\n",
+ "#Reduce the dynamic range\n",
+ "mi += 1.5e7\n",
+ "ma -= 0.81e7"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Create a Transfer Function that goes from the minimum to the maximum of the data:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "tf = ColorTransferFunction((mi, ma), grey_opacity=False)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Define the properties and size of the `camera` viewport:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Choose a vector representing the viewing direction.\n",
+ "L = [0.5, 0.5, 0.5]\n",
+ "# Define the center of the camera to be the domain center\n",
+ "c = pf.domain_center\n",
+ "# Define the width of the image\n",
+ "W = 1.5*pf.domain_width\n",
+ "# Define the number of pixels to render\n",
+ "Npixels = 512 "
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Create a `camera` object and "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "cam = pf.h.camera(c, L, W, Npixels, tf, fields=['Temperature'],\n",
+ " north_vector=[0,0,1], steady_north=True, \n",
+ " sub_samples=5, no_ghost=False,log_fields=False)\n",
+ "\n",
+ "cam.transfer_function.map_to_colormap(mi,ma, \n",
+ " scale=15.0, colormap='algae')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "cam.show()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "heading",
+ "level": 3,
+ "metadata": {},
+ "source": [
"FITS image data"
]
},
diff -r b3f928d031cf9d99317a1aee85c6ee051d0c5c96 -r 62499b35280bf517006308094385fa7f7a946c85 source/visualizing/volume_rendering.rst
--- a/source/visualizing/volume_rendering.rst
+++ b/source/visualizing/volume_rendering.rst
@@ -256,10 +256,10 @@
.. _transfer-function-helper:
-TransferFunctionHelpler
------------------------
+TransferFunctionHelper
+----------------------
-.. notebook:: TransferFunctionHelpler_Tutorial.ipynb
+.. notebook:: TransferFunctionHelper_Tutorial.ipynb
.. _healpix_volume_rendering:
https://bitbucket.org/yt_analysis/yt-doc/commits/c3a9cac0a7d9/
Changeset: c3a9cac0a7d9
User: chummels
Date: 2013-11-22 22:25:35
Summary: Merging.
Affected #: 0 files
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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