[yt-svn] commit/yt-doc: 11 new changesets
Bitbucket
commits-noreply at bitbucket.org
Fri Dec 9 13:37:44 PST 2011
11 new commits in yt-doc:
https://bitbucket.org/yt_analysis/yt-doc/changeset/c60e7caea2fb/
changeset: c60e7caea2fb
user: MatthewTurk
date: 2011-12-09 20:18:20
summary: Adding docs for isocontours.
affected #: 1 file
diff -r a5e377a0e36615922571c168a58c3713090c38d7 -r c60e7caea2fb14ecb62698c8094eede238e21d6e source/analyzing/objects.rst
--- a/source/analyzing/objects.rst
+++ b/source/analyzing/objects.rst
@@ -232,6 +232,65 @@
particle and the baryon mass, so we have two total values passed from the main
function into the collator.
+.. _extracting-connected-sets:
+
+Extracting Connected Sets
+-------------------------
+
+The underlying machinery used in :ref:`clump_finding` is accessible from any
+data object. This includes the ability to obtain and examine topologically
+connected sets. These sets are identified by examining cells between two
+threshold values and connecting them. What is returned to the user is a list
+of the intervals of values found, and extracted regions that contain only those
+cells that are connected.
+
+To use this, call
+:meth:`~yt.data_objects.data_containers.AMR3DData.extract_connected_sets` on
+any 3D data object. This requests a field, the number of levels of levels sets to
+extract, the min and the max value beween which sets will be identified, and
+whether or not to conduct it in log space.
+
+.. code-block:: python
+
+ sp = pf.h.sphere("max", (1.0, 'pc'))
+ contour_values, connected_sets = sp.extract_connected_sets(
+ "Density", 3, 1e-30, 1e-20)
+
+The first item, ``contour_values``, will be an array of the min value for each
+set of level sets. The second (``connected_sets``) will be a dict of dicts.
+The key for the first (outer) dict is the level of the contour, corresponding
+to ``contour_values``. The inner dict returned is keyed by the contour ID. It
+contains :class:`~yt.data_objects.data_containers.AMRExtractedRegionBase`
+objects. These can be queried just as any other data object.
+
+.. _extracting-isocontour-information:
+
+Extracting Isocontour Information
+---------------------------------
+
+.. versionadded:: 2.3
+
+.. warning:: This is still beta!
+
+``yt`` contains an implementation of the `Marching Cubes
+<http://en.wikipedia.org/wiki/Marching_cubes>`_ algorithm, which can operate on
+3D data objects. This provides two pieces of functionality. The first is to
+identify isocontours and return either the geometry of those isocontours or to
+return another field value sampled along that isocontour. The second piece of
+functionality is to calculate the flux of a field over an isocontour.
+
+Note that these isocontours are not guaranteed to be topologically connected.
+In fact, inside a given data object, the marching cubes algorithm will return
+all isocontours, not just a single connected one. This means if you encompass
+two clumps of a given density in your data object and extract an isocontour at
+that density, it will include both of the clumps.
+
+To extract geometry or sample a field, call
+:meth:`yt.data_objects.data_containers.AMR3DData.extract_isocontours`. To
+calculate a flux, call
+:meth:`yt.data_objects.data_containers.AMR3DData.calculate_isocontour_flux`.
+both of these operations will run in parallel.
+
.. _object-serialization:
Storing and Loading Objects
@@ -330,3 +389,4 @@
This method works for clumps, as well, and the entire clump hierarchy will be
stored and restored upon load.
+
https://bitbucket.org/yt_analysis/yt-doc/changeset/2c7e5c29ccb5/
changeset: 2c7e5c29ccb5
branch: yt-2.3
user: MatthewTurk
date: 2011-09-30 16:42:36
summary: Adding off_axis_projection to docstring parses.
affected #: 1 file
diff -r ab9374ab2caddbc4adb75d28a77dbc7467432b64 -r 2c7e5c29ccb565fc9839bbcad7b38d900895dca0 source/reference/api/extension_types.rst
--- a/source/reference/api/extension_types.rst
+++ b/source/reference/api/extension_types.rst
@@ -46,6 +46,7 @@
:toctree: generated/
~yt.visualization.volume_rendering.camera.Camera
+ ~yt.visualization.volume_rendering.off_axis_projection
~yt.visualization.volume_rendering.transfer_functions.ColorTransferFunction
~yt.visualization.volume_rendering.grid_partitioner.HomogenizedVolume
~yt.visualization.volume_rendering.transfer_functions.MultiVariateTransferFunction
https://bitbucket.org/yt_analysis/yt-doc/changeset/f346289bf528/
changeset: f346289bf528
user: MatthewTurk
date: 2011-12-09 20:27:49
summary: Merging from the 2.3 branch.
affected #: 3 files
diff -r c60e7caea2fb14ecb62698c8094eede238e21d6e -r f346289bf528fe13a6e556be81297d29f3863366 source/conf.py
--- a/source/conf.py
+++ b/source/conf.py
@@ -51,9 +51,9 @@
# built documents.
#
# The short X.Y version.
-version = '2.2'
+version = '2.3'
# The full version, including alpha/beta/rc tags.
-release = '2.2'
+release = '2.3dev'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff -r c60e7caea2fb14ecb62698c8094eede238e21d6e -r f346289bf528fe13a6e556be81297d29f3863366 source/interacting/command-line.rst
--- a/source/interacting/command-line.rst
+++ b/source/interacting/command-line.rst
@@ -172,6 +172,15 @@
details), you can create slices and projections easily at the
command-line.
+render
+++++++
+
+This command generates a volume rendering for a single dataset. By sepcifying
+the center, width, number of pixels, number and thickness of contours, etc.
+(run ``yt help render`` for details), you can create high-quality volume
+renderings at the command-line before moving on to more involved volume
+rendering scripts.
+
rpdb
++++
diff -r c60e7caea2fb14ecb62698c8094eede238e21d6e -r f346289bf528fe13a6e556be81297d29f3863366 source/reference/api/extension_types.rst
--- a/source/reference/api/extension_types.rst
+++ b/source/reference/api/extension_types.rst
@@ -46,6 +46,7 @@
:toctree: generated/
~yt.visualization.volume_rendering.camera.Camera
+ ~yt.visualization.volume_rendering.off_axis_projection
~yt.visualization.volume_rendering.transfer_functions.ColorTransferFunction
~yt.visualization.volume_rendering.grid_partitioner.HomogenizedVolume
~yt.visualization.volume_rendering.transfer_functions.MultiVariateTransferFunction
https://bitbucket.org/yt_analysis/yt-doc/changeset/56b6c43fd086/
changeset: 56b6c43fd086
user: MatthewTurk
date: 2011-12-09 20:30:28
summary: Fixing up some API docs
affected #: 1 file
diff -r f346289bf528fe13a6e556be81297d29f3863366 -r 56b6c43fd0860d1960f0c3cd4b17ad874c782be7 source/reference/api/extension_types.rst
--- a/source/reference/api/extension_types.rst
+++ b/source/reference/api/extension_types.rst
@@ -46,7 +46,7 @@
:toctree: generated/
~yt.visualization.volume_rendering.camera.Camera
- ~yt.visualization.volume_rendering.off_axis_projection
+ ~yt.visualization.volume_rendering.camera.off_axis_projection
~yt.visualization.volume_rendering.transfer_functions.ColorTransferFunction
~yt.visualization.volume_rendering.grid_partitioner.HomogenizedVolume
~yt.visualization.volume_rendering.transfer_functions.MultiVariateTransferFunction
@@ -57,7 +57,6 @@
~yt.visualization.volume_rendering.transfer_functions.ProjectionTransferFunction
~yt.visualization.volume_rendering.camera.StereoPairCamera
~yt.visualization.volume_rendering.transfer_functions.TransferFunction
- ~yt.visualization.volume_rendering.software_sampler.VolumeRendering
.. _image_writer:
https://bitbucket.org/yt_analysis/yt-doc/changeset/cae6bcf0b850/
changeset: cae6bcf0b850
user: MatthewTurk
date: 2011-12-09 20:36:58
summary: Fixing a batch of compilation errors.
affected #: 17 files
Diff too large to display.
https://bitbucket.org/yt_analysis/yt-doc/changeset/8648c73df925/
changeset: 8648c73df925
user: MatthewTurk
date: 2011-12-09 20:55:10
summary: Minor change for method name resolution.
affected #: 1 file
diff -r cae6bcf0b8506ca10f59117fbf1df1d746a64b88 -r 8648c73df925b037ed9cbbe7ee4949a299f90c2e source/analyzing/objects.rst
--- a/source/analyzing/objects.rst
+++ b/source/analyzing/objects.rst
@@ -286,9 +286,9 @@
that density, it will include both of the clumps.
To extract geometry or sample a field, call
-:meth:`yt.data_objects.data_containers.AMR3DData.extract_isocontours`. To
+:meth:`~yt.data_objects.data_containers.AMR3DData.extract_isocontours`. To
calculate a flux, call
-:meth:`yt.data_objects.data_containers.AMR3DData.calculate_isocontour_flux`.
+:meth:`~yt.data_objects.data_containers.AMR3DData.calculate_isocontour_flux`.
both of these operations will run in parallel.
.. _object-serialization:
https://bitbucket.org/yt_analysis/yt-doc/changeset/8d9150ff8e36/
changeset: 8d9150ff8e36
user: MatthewTurk
date: 2011-12-09 21:07:25
summary: Responding to comment
affected #: 1 file
diff -r 8648c73df925b037ed9cbbe7ee4949a299f90c2e -r 8d9150ff8e368e7914b36cf33f9add65314d6cb5 source/analyzing/objects.rst
--- a/source/analyzing/objects.rst
+++ b/source/analyzing/objects.rst
@@ -274,9 +274,9 @@
``yt`` contains an implementation of the `Marching Cubes
<http://en.wikipedia.org/wiki/Marching_cubes>`_ algorithm, which can operate on
-3D data objects. This provides two pieces of functionality. The first is to
-identify isocontours and return either the geometry of those isocontours or to
-return another field value sampled along that isocontour. The second piece of
+3D data objects. This provides two things. The first is to identify
+isocontours and return either the geometry of those isocontours or to return
+another field value sampled along that isocontour. The second piece of
functionality is to calculate the flux of a field over an isocontour.
Note that these isocontours are not guaranteed to be topologically connected.
https://bitbucket.org/yt_analysis/yt-doc/changeset/6a8bee89f4f2/
changeset: 6a8bee89f4f2
user: MatthewTurk
date: 2011-12-09 21:40:52
summary: Adding adaptive HEALpix docs.
affected #: 1 file
diff -r 8d9150ff8e368e7914b36cf33f9add65314d6cb5 -r 6a8bee89f4f2b2977c6396454fb7171a1cda3c01 source/visualizing/volume_rendering.rst
--- a/source/visualizing/volume_rendering.rst
+++ b/source/visualizing/volume_rendering.rst
@@ -301,3 +301,48 @@
As it stands, this is still a bit do-it-yourself. Improvements and suggestions
would be welcomed!
+
+.. _healpix_volume_rendering:
+
+Adaptive HEALpix Volume Rendering
+---------------------------------
+.. versionadded:: 2.3
+
+.. warning::
+ This is still in beta. You should verify it gives correct results for your
+ dataset by projecting the field "Ones" and ensuring it is 1.0 everywhere
+ before relying on it for scientific analysis.
+
+In addition to the static-resolution HEALpix volume rendering noted above,
+``yt`` has the object
+:class:`~yt.visualization.volume_rendering.camera.AdaptiveHEALpixCamera`, which
+will traverse grids ensuring adequate covering area at all times. This is
+similar to the MORAY method described in Wise et al 2011. ``yt`` at this time
+does not provide any visualization services for this camera.
+
+To use this, you will need to do some groundwork yourself. An example script
+is listed below. Note that the parameters ``NSide_initial`` and
+``rays_per_cell`` govern how rays split as they move away from the central
+source, and the returned values are a list of the ``NSide`` values and indices
+for a pixel, along with the values accumulated.
+
+.. code-block:: python
+
+ from yt.mods import *
+ from yt.visualization.volume_rendering.camera import \
+ AdaptiveHEALpixCamera
+
+ pf = load("DD0030/data0030")
+ NSide_initial = 32
+ rays_per_cell = 2.0
+
+ v, c = pf.h.find_max("Density")
+ R = 1.0/pf['pc']
+
+ camera = AdaptiveHEALpixCamera(c, R, NSide_initial,
+ fields = ["Density"], log_fields = [False], pf = pf,
+ rays_per_cell = rays_per_cell)
+
+ snap = camera.snapshot()
+ print "NSide", snap[0][:,0].min(), snap[0][:,0].max(), snap[0].shape
+ print "Vals", snap[1][:,3].min(), snap[1][:,3].max()
https://bitbucket.org/yt_analysis/yt-doc/changeset/aff9fb58470a/
changeset: aff9fb58470a
user: MatthewTurk
date: 2011-12-09 21:41:49
summary: Adding a note about making it more user-friendly.
affected #: 1 file
diff -r 6a8bee89f4f2b2977c6396454fb7171a1cda3c01 -r aff9fb58470ad80e89f1c9a3a15904aa117da7bc source/visualizing/volume_rendering.rst
--- a/source/visualizing/volume_rendering.rst
+++ b/source/visualizing/volume_rendering.rst
@@ -346,3 +346,7 @@
snap = camera.snapshot()
print "NSide", snap[0][:,0].min(), snap[0][:,0].max(), snap[0].shape
print "Vals", snap[1][:,3].min(), snap[1][:,3].max()
+
+With future versions of ``yt``, this functionality will become more
+user-friendly. If you would like to participate in this effort, that would be
+awesome. See :ref:`contributing-code` for more info.
https://bitbucket.org/yt_analysis/yt-doc/changeset/175273fdcbe1/
changeset: 175273fdcbe1
user: MatthewTurk
date: 2011-12-09 21:54:13
summary: Adding 2.3 changelog.
affected #: 2 files
diff -r aff9fb58470ad80e89f1c9a3a15904aa117da7bc -r 175273fdcbe1a78f042cf4fbf8100442849778f5 source/reference/changelog.rst
--- a/source/reference/changelog.rst
+++ b/source/reference/changelog.rst
@@ -5,6 +5,26 @@
This is a non-comprehensive log of changes to the code.
+Version 2.3
+-----------
+
+ * Multi-level parallelism
+ * Real, extensive answer tests
+ * Boolean data regions (see :ref:`boolean_data_objects`)
+ * Isocontours / flux calculations (see :ref:`extracting-isocontour-information`)
+ * Field reorganization (see :ref:`types-of-fields`)
+ * PHOP memory improvements
+ * Bug fixes for tests
+ * Parallel data loading for RAMSES, along with other speedups and improvements
+ there
+ * Performance improvements for volume rendering
+ * Adaptive HEALpix support (see :ref:`adaptive_healpix_volume_rendering`)
+ * Column density calculations (see :ref:`radial_column_density`)
+ * Massive speedup for 1D profiles
+ * Lots more, bug fixes etc.
+ * Substantial improvements to the documentation, including
+ :ref:`manual-plotting` and a revamped :ref:`orientation`.
+
Version 2.2
-----------
diff -r aff9fb58470ad80e89f1c9a3a15904aa117da7bc -r 175273fdcbe1a78f042cf4fbf8100442849778f5 source/visualizing/volume_rendering.rst
--- a/source/visualizing/volume_rendering.rst
+++ b/source/visualizing/volume_rendering.rst
@@ -302,7 +302,7 @@
As it stands, this is still a bit do-it-yourself. Improvements and suggestions
would be welcomed!
-.. _healpix_volume_rendering:
+.. _adaptive_healpix_volume_rendering:
Adaptive HEALpix Volume Rendering
---------------------------------
https://bitbucket.org/yt_analysis/yt-doc/changeset/656e0e35d068/
changeset: 656e0e35d068
user: MatthewTurk
date: 2011-12-09 22:01:55
summary: Fixing cross-references
affected #: 2 files
diff -r 175273fdcbe1a78f042cf4fbf8100442849778f5 -r 656e0e35d068345bad4259fa27c73c1d6eee6e85 source/analyzing/objects.rst
--- a/source/analyzing/objects.rst
+++ b/source/analyzing/objects.rst
@@ -149,7 +149,7 @@
.. include:: _obj_docstrings.inc
-.. _boolean_data_objects
+.. _boolean_data_objects:
Boolean Data Objects
--------------------
diff -r 175273fdcbe1a78f042cf4fbf8100442849778f5 -r 656e0e35d068345bad4259fa27c73c1d6eee6e85 source/reference/changelog.rst
--- a/source/reference/changelog.rst
+++ b/source/reference/changelog.rst
@@ -12,7 +12,7 @@
* Real, extensive answer tests
* Boolean data regions (see :ref:`boolean_data_objects`)
* Isocontours / flux calculations (see :ref:`extracting-isocontour-information`)
- * Field reorganization (see :ref:`types-of-fields`)
+ * Field reorganization (see :ref:`types_of_fields`)
* PHOP memory improvements
* Bug fixes for tests
* Parallel data loading for RAMSES, along with other speedups and improvements
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the yt-svn
mailing list