[yt-svn] commit/yt-doc: 2 new changesets
Bitbucket
commits-noreply at bitbucket.org
Wed Dec 14 10:49:08 PST 2011
2 new commits in yt-doc:
https://bitbucket.org/yt_analysis/yt-doc/changeset/5408a9cd438b/
changeset: 5408a9cd438b
user: MatthewTurk
date: 2011-12-14 19:26:01
summary: Re-ran the helper scripts for objects, derived quantities, and callbacks
affected #: 6 files
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 helper_scripts/parse_cb_list.py
--- a/helper_scripts/parse_cb_list.py
+++ b/helper_scripts/parse_cb_list.py
@@ -2,7 +2,7 @@
import inspect
from textwrap import TextWrapper
-pf = load("/Users/matthewturk/Research/data/RD0005-mine/RedshiftOutput0005")
+pf = load("RD0005-mine/RedshiftOutput0005")
output = open("source/visualizing/_cb_docstrings.inc", "w")
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 helper_scripts/parse_dq_list.py
--- a/helper_scripts/parse_dq_list.py
+++ b/helper_scripts/parse_dq_list.py
@@ -2,7 +2,7 @@
import inspect
from textwrap import TextWrapper
-pf = load("/Users/matthewturk/Research/data/RD0005-mine/RedshiftOutput0005")
+pf = load("RD0005-mine/RedshiftOutput0005")
output = open("source/analyzing/_dq_docstrings.inc", "w")
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 helper_scripts/parse_object_list.py
--- a/helper_scripts/parse_object_list.py
+++ b/helper_scripts/parse_object_list.py
@@ -2,7 +2,7 @@
import inspect
from textwrap import TextWrapper
-pf = load("/home/jsoishi/data/enzo/RD0005-mine/RedshiftOutput0005")
+pf = load("RD0005-mine/RedshiftOutput0005")
output = open("source/analyzing/_obj_docstrings.inc", "w")
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 source/analyzing/_dq_docstrings.inc
--- a/source/analyzing/_dq_docstrings.inc
+++ b/source/analyzing/_dq_docstrings.inc
@@ -35,11 +35,19 @@
-.. function:: CenterOfMass():
+.. function:: CenterOfMass(use_cells=True, use_particles=False):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._CenterOfMass`.)
- This function takes no arguments and returns the location of the center
- of mass of the *non-particle* data in the object.
+ This function returns the location of the center
+ of mass. By default, it computes of the *non-particle* data in the object.
+
+ Parameters
+ ----------
+
+ use_cells : bool
+ If True, will include the cell mass (default: True)
+ use_particles : bool
+ if True, will include the particles in the object (default: False)
@@ -53,30 +61,57 @@
-.. function:: IsBound(truncate=True, include_thermal_energy=False):
+.. function:: IsBound(truncate=True, include_thermal_energy=False, treecode=True, opening_angle=1.0, periodic_test=False, include_particles=True):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._IsBound`.)
- This returns whether or not the object is gravitationally bound
+ This returns whether or not the object is gravitationally bound. If this
+ returns a value greater than one, it is bound, and otherwise not.
- :param truncate: Should the calculation stop once the ratio of
- gravitational:kinetic is 1.0?
- :param include_thermal_energy: Should we add the energy from ThermalEnergy
- on to the kinetic energy to calculate
- binding energy?
+ Parameters
+ ----------
+ truncate : Bool
+ Should the calculation stop once the ratio of
+ gravitational:kinetic is 1.0?
+ include_thermal_energy : Bool
+ Should we add the energy from ThermalEnergy
+ on to the kinetic energy to calculate
+ binding energy?
+ treecode : Bool
+ Whether or not to use the treecode.
+ opening_angle : Float
+ The maximal angle a remote node may subtend in order
+ for the treecode method of mass conglomeration may be
+ used to calculate the potential between masses.
+ periodic_test : Bool
+ Used for testing the periodic adjustment machinery
+ of this derived quantity.
+ include_particles : Bool
+ Should we add the mass contribution of particles
+ to calculate binding energy?
+
+ Examples
+ --------
+ >>> sp.quantities["IsBound"](truncate=False,
+ ... include_thermal_energy=True, treecode=False, opening_angle=2.0)
+ 0.32493
.. function:: MaxLocation(field):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._MaxLocation`.)
- This function returns six values: the maximum value of a set
- of fields, the index of that maximum, its three physical coordinate
- location and the index of the grid it is on.
+ This function returns the location of the maximum of a set
+ of fields.
+
+
.. function:: MinLocation(field):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._MinLocation`.)
- As above but for the minimum point of a field.
+ This function returns the location of the minimum of a set
+ of fields.
+
+
.. function:: ParticleSpinParameter():
@@ -86,6 +121,14 @@
+.. function:: StarAngularMomentumVector():
+
+ (This is a proxy for :func:`~yt.data_objects.derived_quantities._StarAngularMomentumVector`.)
+ This function returns the mass-weighted average angular momentum vector
+ for stars.
+
+
+
.. function:: TotalMass():
(This is a proxy for :func:`~yt.data_objects.derived_quantities._TotalMass`.)
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 source/analyzing/_obj_docstrings.inc
--- a/source/analyzing/_obj_docstrings.inc
+++ b/source/analyzing/_obj_docstrings.inc
@@ -1,120 +1,126 @@
+
+
+.. class:: boolean(self, regions, fields=None, pf=None, **field_parameters):
+
+ For more information, see :ref:`physical-object-api`
+ (This is a proxy for :class:`~yt.data_objects.data_containers.AMRBooleanRegionBase`.)
.. class:: covering_grid(self, level, left_edge, dims, fields=None, pf=None, num_ghost_zones=0, use_pbar=True, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRCoveringGridBase`.)
.. class:: cutting(self, normal, center, fields=None, node_name=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRCuttingPlaneBase`.)
.. class:: disk(self, center, normal, radius, height, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRCylinderBase`.)
.. class:: extracted_region(self, base_region, indices, force_refresh=True, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.ExtractedRegionBase`.)
.. class:: fixed_res_cutting(self, normal, center, width, dims, fields=None, node_name=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRFixedResCuttingPlaneBase`.)
.. class:: fixed_res_proj(self, axis, level, left_edge, dims, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRFixedResProjectionBase`.)
.. class:: grid_collection(self, center, grid_list, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRGridCollectionBase`.)
.. class:: inclined_box(self, origin, box_vectors, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRInclinedBoxBase`.)
.. class:: ortho_ray(self, axis, coords, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMROrthoRayBase`.)
.. class:: overlap_proj(self, axis, field, weight_field=None, max_level=None, center=None, pf=None, source=None, node_name=None, field_cuts=None, preload_style='level', serialize=True, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRProjBase`.)
.. class:: periodic_region(self, center, left_edge, right_edge, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRPeriodicRegionBase`.)
.. class:: periodic_region_strict(self, center, left_edge, right_edge, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRPeriodicRegionStrictBase`.)
.. class:: proj(self, axis, field, weight_field=None, max_level=None, center=None, pf=None, source=None, node_name=None, field_cuts=None, preload_style='level', serialize=True, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRQuadTreeProjBase`.)
.. class:: ray(self, start_point, end_point, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRRayBase`.)
.. class:: region(self, center, left_edge, right_edge, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRRegionBase`.)
.. class:: region_strict(self, center, left_edge, right_edge, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRRegionStrictBase`.)
.. class:: slice(self, axis, coord, fields=None, center=None, pf=None, node_name=False, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRSliceBase`.)
.. class:: smoothed_covering_grid(self, *args, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRSmoothedCoveringGridBase`.)
.. class:: sphere(self, center, radius, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRSphereBase`.)
.. class:: streamline(self, positions, fields=None, pf=None, **field_parameters):
-For more information, see :ref:`physical-object-api`
+ For more information, see :ref:`physical-object-api`
(This is a proxy for :class:`~yt.data_objects.data_containers.AMRStreamlineBase`.)
diff -r a4e2a32822efc825df8b805b0f32f2e9cdac75cf -r 5408a9cd438b1fecd3034ef913378deb95244d74 source/visualizing/_cb_docstrings.inc
--- a/source/visualizing/_cb_docstrings.inc
+++ b/source/visualizing/_cb_docstrings.inc
@@ -65,13 +65,12 @@
(This is a proxy for :class:`~yt.visualization.plot_modifications.HopCircleCallback`.)
- Accepts a :class:`yt.HopList` *hop_output* and
- plots up to *max_number* (None for unlimited) halos as
- circles.
+ Accepts a :class:`yt.HopList` *hop_output* and plots up
+ to *max_number* (None for unlimited) halos as circles.
-.. function:: hop_particles(self, hop_output, p_size=1.0, max_number=None, min_size=20, alpha=0.20000000000000001):
+.. function:: hop_particles(self, hop_output, max_number, p_size=1.0, min_size=20, alpha=0.2):
(This is a proxy for :class:`~yt.visualization.plot_modifications.HopParticleCallback`.)
@@ -83,7 +82,7 @@
-.. function:: image_line(self, p1, p2, plot_args=None):
+.. function:: image_line(self, p1, p2, data_coords=False, plot_args=None):
(This is a proxy for :class:`~yt.visualization.plot_modifications.ImageLineCallback`.)
@@ -100,17 +99,6 @@
-.. function:: level_grids(self, level, alpha=1.0, min_pix=1, annotate=False, periodic=True, color=(0.0, 0.0, 0.0)):
-
- (This is a proxy for :class:`~yt.visualization.plot_modifications.LevelGridBoundaryCallback`.)
-
- Adds grid boundaries from a given *level* to a plot,
- optionally with *alpha*-blending. Cuttoff for display is
- at *min_pix* wide. *annotate* puts the grid id in the
- corner of the grid, and *color* specifies the color.
-
-
-
.. function:: line(self, x, y, plot_args=None):
(This is a proxy for :class:`~yt.visualization.plot_modifications.LinePlotCallback`.)
@@ -119,12 +107,18 @@
-.. function:: magnetic_field(self, factor=16):
+.. function:: magnetic_field(self, factor=16, scale=None, scale_units=None, normalize=False):
(This is a proxy for :class:`~yt.visualization.plot_modifications.MagFieldCallback`.)
Adds a 'quiver' plot of magnetic field to the plot,
- skipping all but every *factor* datapoint
+ skipping all but every *factor* datapoint. *scale* is the
+ data units per arrow length unit using *scale_units* (see
+ matplotlib.axes.Axes.quiver for more info). if
+ *normalize* is True, the magnetic fields will be scaled
+ by their local (in-plane) length, allowing morphological
+ features to be more clearly seen for fields with
+ substantial variation in field strength.
@@ -163,13 +157,15 @@
-.. function:: quiver(self, field_x, field_y, factor):
+.. function:: quiver(self, field_x, field_y, factor, scale=None, scale_units=None, normalize=False):
(This is a proxy for :class:`~yt.visualization.plot_modifications.QuiverCallback`.)
Adds a 'quiver' plot to any plot, using the *field_x* and
*field_y* from the associated data, skipping every
- *factor* datapoints.
+ *factor* datapoints *scale* is the data units per arrow
+ length unit using *scale_units* (see
+ matplotlib.axes.Axes.quiver for more info)
@@ -197,12 +193,14 @@
-.. function:: text(self, pos, text, text_args=None):
+.. function:: text(self, pos, text, data_coords=False, text_args=None):
(This is a proxy for :class:`~yt.visualization.plot_modifications.TextLabelCallback`.)
Accepts a position in (0..1, 0..1) of the image, some
- text and optionally some text arguments.
+ text and optionally some text arguments. If data_coords
+ is True, position will be in code units instead of image
+ coordinates.
@@ -224,12 +222,19 @@
-.. function:: velocity(self, factor=16):
+.. function:: velocity(self, factor=16, scale=None, scale_units=None, normalize=False):
(This is a proxy for :class:`~yt.visualization.plot_modifications.VelocityCallback`.)
Adds a 'quiver' plot of velocity to the plot, skipping
- all but every *factor* datapoint
+ all but every *factor* datapoint. *scale* is the data
+ units per arrow length unit using *scale_units* (see
+ matplotlib.axes.Axes.quiver for more info). if
+ *normalize* is True, the velocity fields will be scaled
+ by their local (in-plane) length, allowing morphological
+ features to be more clearly seen for fields with
+ substantial variation in field strength (normalize is not
+ implemented and thus ignored for Cutting Planes).
@@ -237,6 +242,6 @@
(This is a proxy for :class:`~yt.visualization.plot_modifications.VobozCircleCallback`.)
- x.__init__(...) initializes x; see x.__class__.__doc__
- for signature
+ x.__init__(...) initializes x; see help(type(x)) for
+ signature
https://bitbucket.org/yt_analysis/yt-doc/changeset/5b9c86452b83/
changeset: 5b9c86452b83
user: MatthewTurk
date: 2011-12-14 19:42:14
summary: Updating the .inc files for the cookbook.
affected #: 10 files
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -5,3 +5,4 @@
build/*
source/reference/api/generated/*
**/.DS_Store
+RD0005-mine/*
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e helper_scripts/update_recipes.py
--- a/helper_scripts/update_recipes.py
+++ b/helper_scripts/update_recipes.py
@@ -43,6 +43,7 @@
title = ".. _cookbook-%s:\n\n%s" % (fn, title)
if lines[0] != '"""':
print " Bad docstring: breaking."
+ print file
di = lines[1:].index('"""')
docstring = lines[1:di+1]
recipe = lines[di+2:]
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/camera_movement.inc
--- a/source/cookbook/camera_movement.inc
+++ b/source/cookbook/camera_movement.inc
@@ -59,4 +59,10 @@
+.. rubric:: Sample Output
+.. image:: _camera_movement/camera_movement_camera_movement_0029.png
+ :width: 240
+ :target: ../_images/camera_movement_camera_movement_0029.png
+
+
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/find_clumps.inc
--- a/source/cookbook/find_clumps.inc
+++ b/source/cookbook/find_clumps.inc
@@ -59,15 +59,5 @@
# the "clumps" callback on a plot.
-.. rubric:: Sample Output
-``RedshiftOutput0005_clump_hierarchy.txt``
-
-.. literalinclude:: _find_clumps/find_clumps_RedshiftOutput0005_clump_hierarchy.txt
-
-``RedshiftOutput0005_clumps.txt``
-
-.. literalinclude:: _find_clumps/find_clumps_RedshiftOutput0005_clumps.txt
-
-
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/halo_finding.inc
--- a/source/cookbook/halo_finding.inc
+++ b/source/cookbook/halo_finding.inc
@@ -3,7 +3,7 @@
Halo finding
------------
-This script shows the simples way of getting halo information. For more
+This script shows the simplest way of getting halo information. For more
information, see :ref:`halo_finding`.
The latest version of this recipe can be downloaded here: http://hg.yt-project.org/cookbook/raw/tip/recipes/halo_finding.py .
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/make_light_ray.inc
--- a/source/cookbook/make_light_ray.inc
+++ b/source/cookbook/make_light_ray.inc
@@ -3,62 +3,69 @@
Make light ray
--------------
-The following example will make a light ray (see :ref:`light-ray-generator`) from
-z = 0 to z = 0.1. In this example, we will also get the distance and mass of the
-halo nearest to every element of the ray.
+This is a recipe to make a light ray through a simulation.
The latest version of this recipe can be downloaded here: http://hg.yt-project.org/cookbook/raw/tip/recipes/make_light_ray.py .
.. code-block:: python
- import os
- import sys
-
- from yt.mods import *
- from yt.analysis_modules.halo_profiler.api import *
- from yt.analysis_modules.light_ray.api import *
-
- # Get the simulation parameter file from the command line.
- par_file = sys.argv[1]
-
- # Instantiate a ray object from z = 0 to z = 0.1 using the
- # minimum number of datasets.
- lr = LightRay(par_file, 0.0, 0.1, use_minimum_datasets=True)
-
- # The next three variable are used when get_nearest_galaxy is set to True.
- # This option will calculate the distance and mass of the halo nearest to
- # each element of the ray.
- # The light ray tool accomplishes this by using the HaloProfiler.
- # Here we are providing the LightRay with instructions to give the HaloProfiler.
- # This is a dictionary of standard halo profiler keyword arguments and values.
- halo_profiler_kwargs = {'halo_list_format': {'id':0, 'center':[4, 5, 6],
- 'TotalMassMsun':1},
- 'halo_list_file': 'HopAnalysis.out'}
- # This is a list of actions we want the HaloProfiler to perform.
- # Note that each list item (only one item in this example) is a dictionary
- # with the following three entries: 'function', 'args', and 'kwargs'.
- # These are the function to be called, the arguments to that function, and
- # any keyword arguments.
- halo_profiler_actions = [{'function': make_profiles,
- 'args': None,
- 'kwargs': {'filename': 'VirializedHalos.out'}}]
- # This option can only be 'all' or 'filtered' and tells the HaloProfiler to
- # use either the full halo list or the filtered list made after calling make_profiles.
- halo_list = 'filtered'
+ import os
+ import sys
- # This is the name of the field from the halo list that represents the halo mass.
- halo_mass_field = 'TotalMassMsun_200'
+ from yt.mods import *
+ from yt.analysis_modules.halo_profiler.api import *
+ from yt.analysis_modules.light_ray.api import *
- # Make the ray and get the Density and Temperature fields, the nearest galaxy information, and
- # the line of sight velocity.
- lr.make_light_ray(seed=8675309,
- solution_filename='lightraysolution.txt',
- data_filename='lightray.h5',
- fields=['Temperature', 'Density'],
- get_nearest_galaxy=True,
- halo_profiler_kwargs=halo_profiler_kwargs,
- halo_profiler_actions=halo_profiler_actions,
- halo_list=halo_list,
- halo_mass_field=halo_mass_field,
- get_los_velocity=True)
+ # Get the simulation parameter file from the command line.
+ par_file = sys.argv[1]
+
+ # Instantiate a ray object from z = 0 to z = 0.1 using the
+ # minimum number of datasets.
+ lr = LightRay(par_file, 0.0, 0.1, use_minimum_datasets=True)
+
+ # The next four variables are used when get_nearest_galaxy is set to True.
+ # This option will calculate the distance and mass of the halo nearest to
+ # each element of the ray.
+ # The light ray tool accomplishes this by using the HaloProfiler.
+ # Here we are providing the LightRay with instructions to give the HaloProfiler.
+ # This is a dictionary of standard halo profiler keyword arguments and values.
+ halo_profiler_kwargs = {'halo_list_format': {'id':0, 'center':[4, 5, 6],
+ 'TotalMassMsun':1},
+ 'halo_list_file': 'HopAnalysis.out'}
+ # This is a list of actions we want the HaloProfiler to perform.
+ # Note that each list item is a dictionary with the following three
+ # entries: 'function', 'args', and 'kwargs'.
+ # These are the function to be called, the arguments to that function, and
+ # any keyword arguments.
+ halo_profiler_actions = [{'function': make_profiles,
+ 'args': None,
+ 'kwargs': {'filename': 'VirializedHalos.out'}},
+ {'function': add_halo_filter,
+ 'args': VirialFilter,
+ 'kwargs': {'overdensity_field': 'ActualOverdensity',
+ 'virial_overdensity': 200,
+ 'virial_filters': [['TotalMassMsun','>=','1e14']],
+ 'virial_quantities': ['TotalMassMsun','RadiusMpc']}}]
+ # This option can only be 'all' or 'filtered' and tells the HaloProfiler to
+ # use either the full halo list or the filtered list made after calling make_profiles.
+ halo_list = 'filtered'
+
+ # This is the name of the field from the halo list that represents the halo mass.
+ halo_mass_field = 'TotalMassMsun_200'
+
+ # Make the ray and get the Density and Temperature fields, the nearest galaxy information, and
+ # the line of sight velocity.
+ lr.make_light_ray(seed=8675309,
+ solution_filename='lightraysolution.txt',
+ data_filename='lightray.h5',
+ fields=['Temperature', 'Density'],
+ get_nearest_galaxy=True,
+ halo_profiler_kwargs=halo_profiler_kwargs,
+ halo_profiler_actions=halo_profiler_actions,
+ halo_list=halo_list,
+ halo_mass_field=halo_mass_field,
+ get_los_velocity=True)
+
+
+
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/offaxis_projection.inc
--- a/source/cookbook/offaxis_projection.inc
+++ b/source/cookbook/offaxis_projection.inc
@@ -3,12 +3,10 @@
Offaxis projection
------------------
-This recipe shows how to volume render a dataset. There are a number of
-twiddles, and rough edges, and the process is still very much in beta.
+This recipe shows how to make a projection of a dataset from an arbitrary
+projection angle (so you are not confined to the x, y, and z axes).
See :ref:`volume_rendering` for more information.
-Additionally, for the purposes of the recipe, we have simplified the image
-considerably.
The latest version of this recipe can be downloaded here: http://hg.yt-project.org/cookbook/raw/tip/recipes/offaxis_projection.py .
@@ -20,14 +18,6 @@
pf = load(fn) # load data
- # This operates on a pass-through basis, so you should not need to specify
- # limits.
- tf = ProjectionTransferFunction()
-
- # We don't want to take the log of Density, so we need to disable that here.
- # Note that if using the Camera interface, this does not need to be done.
- pf.field_info["Density"].take_log=False
-
# Now we need a center of our volume to render. Here we'll just use
# 0.5,0.5,0.5, because volume renderings are not periodic.
c = [0.5, 0.5, 0.5]
@@ -44,21 +34,20 @@
W = 0.8
# Now we decide how big an image we want. 512x512 should be sufficient.
- Nvec = 512
+ N = 512
- # Now we call the ray caster, which handles the rest.
- # Note that we feed whole_box, which means that it won't apply any cuts to the
- # considered grids. This may be unnecessary for most appliations.
- vp = pf.h.volume_rendering(L, W, c, Nvec, tf, whole_box=True)
+ # Now we call the off_axis_projection function, which handles the rest.
+ # Note that we set no_ghost equal to False, so that we *do* include ghost
+ # zones in our data. This takes longer to calculate, but the results look
+ # much cleaner than when you ignore the ghost zones.
+ # Also note that we set the field which we want to project as "Density", but
+ # really we could use any arbitrary field like "Temperature", "Metallicity"
+ # or whatever.
+ image = off_axis_projection(pf, c, L, W, N, "Density", no_ghost=False)
- # Now we tell the volume rendering object to cast the rays
- vp.ray_cast()
-
- # All the channels are the same, so we only grab one.
- image = na.log10(vp.image[:,:,0])
-
+ # Image is now an NxN array representing the intensities of the various pixels.
# And now, we call our direct image saver. We save the log of the result.
- write_image(image, "%s_offaxis_projection.png" % pf)
+ write_image(na.log10(image), "%s_offaxis_projection.png" % pf)
.. rubric:: Sample Output
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/simple_projection.inc
--- a/source/cookbook/simple_projection.inc
+++ b/source/cookbook/simple_projection.inc
@@ -4,8 +4,9 @@
-----------------
This is a simple recipe to show how to open a dataset and then take a
-weighted-average projection through it, centered at its most dense point. For
-more information see :ref:`methods-projections`.
+weighted-average projection through it, centered at its most dense point.
+This will only project along grid axes (i.e. x,y,z). In order to do
+project along arbitrary projection angles, see the entry for Offaxis Projections. For more information see :ref:`methods-projections`.
The latest version of this recipe can be downloaded here: http://hg.yt-project.org/cookbook/raw/tip/recipes/simple_projection.py .
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/cookbook/simple_volume_rendering.inc
--- a/source/cookbook/simple_volume_rendering.inc
+++ b/source/cookbook/simple_volume_rendering.inc
@@ -3,11 +3,9 @@
Simple volume rendering
-----------------------
-This recipe shows how to volume render a dataset. There are a number of
-twiddles, and rough edges, and the process is still very much in beta.
-See :ref:`volume_rendering` for more information. In particular, this
-interface will do some things very easily, but it provides almost no
-customizability. The Camera interface is recommended.
+This recipe shows how to volume render a dataset.
+See :ref:`volume_rendering` for more information, as there is considerably more
+functionality than is demonstrated here.
Additionally, for the purposes of the recipe, we have simplified the image
considerably.
@@ -71,12 +69,8 @@
# Othwerwise, we can then write out the image using our direct bitmap writer
write_bitmap(image, "%s_volume_rendered.png" % pf)
+
+
-.. rubric:: Sample Output
-.. image:: _simple_volume_rendering/simple_volume_rendering_RedshiftOutput0005_volume_rendered.png
- :width: 240
- :target: ../_images/simple_volume_rendering_RedshiftOutput0005_volume_rendered.png
-
-
diff -r 5408a9cd438b1fecd3034ef913378deb95244d74 -r 5b9c86452b8307e33e90986e1ea63a8858deec8e source/orientation/index.rst
--- a/source/orientation/index.rst
+++ b/source/orientation/index.rst
@@ -20,7 +20,7 @@
* `Dive Into Python <http://diveintopython.org>`_
If you encounter any problems here, or anywhere in yt, please visit the
-:ref:`_asking-for-help` page to figure out a solution.
+:ref:`asking-for-help` page to figure out a solution.
.. toctree::
:maxdepth: 2
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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