[yt-svn] commit/yt: ngoldbaum: Merged in jzuhone/yt-3.x/yt-3.0 (pull request #918)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon May 26 13:53:38 PDT 2014
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/aef63614854a/
Changeset: aef63614854a
Branch: yt-3.0
User: ngoldbaum
Date: 2014-05-26 22:53:31
Summary: Merged in jzuhone/yt-3.x/yt-3.0 (pull request #918)
Slight refactoring of the way PPVCube handles fields, and spiffed up the notebook a bit.
Affected #: 3 files
diff -r 3c7983a318d58fcd39b65eaf24198a3d03e0cb19 -r aef63614854a28effe3680c931e5b6d26475474f doc/source/analyzing/analysis_modules/PPVCube.ipynb
--- a/doc/source/analyzing/analysis_modules/PPVCube.ipynb
+++ b/doc/source/analyzing/analysis_modules/PPVCube.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:3a720e0a18272564522f9fc23553431908d6f2b4f3e3e7dfe5b3e690e2e37677"
+ "signature": "sha256:3f810954006851303837edb8fd85ee6583a883122b0f4867903562546c4f19d2"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -16,6 +16,18 @@
]
},
{
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "%matplotlib inline\n",
+ "from yt.mods import *\n",
+ "from yt.analysis_modules.api import PPVCube"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
"cell_type": "markdown",
"metadata": {},
"source": [
@@ -44,30 +56,40 @@
]
},
{
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "First, we'll set up the grid and the parameters of the profiles:"
+ ]
+ },
+ {
"cell_type": "code",
"collapsed": false,
"input": [
- "%matplotlib inline\n",
- "from yt.mods import *\n",
- "from yt.analysis_modules.api import PPVCube"
+ "nx,ny,nz = (256,256,256) # domain dimensions\n",
+ "R = 10. # outer radius of disk, kpc\n",
+ "r_0 = 3. # scale radius, kpc\n",
+ "beta = 1.4 # for the tangential velocity profile\n",
+ "alpha = -1. # for the radial density profile\n",
+ "x, y = np.mgrid[-R:R:nx*1j,-R:R:ny*1j] # cartesian coordinates of x-y plane of disk\n",
+ "r = np.sqrt(x*x+y*y) # polar coordinates\n",
+ "theta = np.arctan2(y, x) # polar coordinates"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Second, we'll construct the data arrays for the density and the velocity of the disk. Since we have the tangential velocity profile, we have to use the polar coordinates we derived earlier to compute `velx` and `vely`. Everywhere outside the disk, all fields are set to zero. "
+ ]
+ },
+ {
"cell_type": "code",
"collapsed": false,
"input": [
- "data = {}\n",
- "nx,ny,nz = (256,256,256)\n",
- "R = 10. # kpc\n",
- "r_0 = 3. # kpc\n",
- "beta = 1.4\n",
- "alpha = -1.\n",
- "x, y = np.mgrid[-R:R:nx*1j,-R:R:ny*1j] # cartesian coordinates\n",
- "r = np.sqrt(x*x+y*y) # polar coordinates\n",
- "theta = np.arctan2(y, x) # polar coordinates\n",
"dens = np.zeros((nx,ny,nz))\n",
"dens[:,:,nz/2-3:nz/2+3] = (r**alpha).reshape(nx,ny,1) # the density profile of the disk\n",
"vel_theta = r/(1.+(r/r_0)**beta) # the azimuthal velocity profile of the disk\n",
@@ -75,11 +97,31 @@
"vely = np.zeros((nx,ny,nz))\n",
"velx[:,:,nz/2-3:nz/2+3] = (-vel_theta*np.sin(theta)).reshape(nx,ny,1) # convert polar to cartesian\n",
"vely[:,:,nz/2-3:nz/2+3] = (vel_theta*np.cos(theta)).reshape(nx,ny,1) # convert polar to cartesian\n",
+ "dens[r > R] = 0.0\n",
+ "velx[r > R] = 0.0\n",
+ "vely[r > R] = 0.0"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Finally, we'll package these data arrays up into a dictionary, which will then be shipped off to `load_uniform_grid`. We'll define the width of the grid to be `2*R` kpc, which will be equal to 1 `code_length`. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "data = {}\n",
"data[\"density\"] = (dens,\"g/cm**3\")\n",
"data[\"velocity_x\"] = (velx, \"km/s\")\n",
"data[\"velocity_y\"] = (vely, \"km/s\")\n",
"data[\"velocity_z\"] = (np.zeros((nx,ny,nz)), \"km/s\") # zero velocity in the z-direction\n",
- "bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]])\n",
+ "bbox = np.array([[-0.5,0.5],[-0.5,0.5],[-0.5,0.5]]) # bbox of width 1 on a side with center (0,0,0)\n",
"ds = load_uniform_grid(data, (nx,ny,nz), length_unit=(2*R,\"kpc\"), nprocs=1, bbox=bbox)"
],
"language": "python",
@@ -146,7 +188,7 @@
"cell_type": "code",
"collapsed": false,
"input": [
- "cube = PPVCube(ds, L, \"density\", dims=(200,100,50), velocity_bounds=(-0.5,0.5,\"km/s\"))"
+ "cube = PPVCube(ds, L, \"density\", dims=(200,100,50), velocity_bounds=(-1.5,1.5,\"km/s\"))"
],
"language": "python",
"metadata": {},
@@ -180,8 +222,18 @@
"cell_type": "code",
"collapsed": false,
"input": [
- "ds = load(\"cube.fits\")\n",
- "slc = SlicePlot(ds, \"z\", [\"density\"], center=\"c\") # sliced at the center of the domain\n",
+ "pf = load(\"cube.fits\")"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "# Specifying no center gives us the center slice\n",
+ "slc = SlicePlot(pf, \"z\", [\"density\"])\n",
"slc.show()"
],
"language": "python",
@@ -192,19 +244,11 @@
"cell_type": "code",
"collapsed": false,
"input": [
- "# To figure out what the domain center and width is in pixel (code length) units:\n",
- "print ds.domain_center\n",
- "print ds.domain_width"
- ],
- "language": "python",
- "metadata": {},
- "outputs": []
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "slc = SlicePlot(ds, \"z\", [\"density\"], center=[100.5,50.5,-250.0]) # \"z\" slice is in m/s\n",
+ "import yt.units as u\n",
+ "# Picking different velocities for the slices\n",
+ "new_center = pf.domain_center\n",
+ "new_center[2] = pf.spec2pixel(-1.0*u.km/u.s)\n",
+ "slc = SlicePlot(pf, \"z\", [\"density\"], center=new_center)\n",
"slc.show()"
],
"language": "python",
@@ -215,7 +259,8 @@
"cell_type": "code",
"collapsed": false,
"input": [
- "slc = SlicePlot(ds, \"z\", [\"density\"], center=[100.5,50.5,300.0])\n",
+ "new_center[2] = pf.spec2pixel(0.7*u.km/u.s)\n",
+ "slc = SlicePlot(pf, \"z\", [\"density\"], center=new_center)\n",
"slc.show()"
],
"language": "python",
@@ -225,7 +270,31 @@
{
"cell_type": "code",
"collapsed": false,
- "input": [],
+ "input": [
+ "new_center[2] = pf.spec2pixel(-0.3*u.km/u.s)\n",
+ "slc = SlicePlot(pf, \"z\", [\"density\"], center=new_center)\n",
+ "slc.show()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "If we project all the emission at all the different velocities along the z-axis, we recover the entire disk:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "prj = ProjectionPlot(pf, \"z\", [\"density\"], proj_style=\"sum\")\n",
+ "prj.set_log(\"density\", True)\n",
+ "prj.set_zlim(\"density\", 1.0e-3, 0.2)\n",
+ "prj.show()"
+ ],
"language": "python",
"metadata": {},
"outputs": []
diff -r 3c7983a318d58fcd39b65eaf24198a3d03e0cb19 -r aef63614854a28effe3680c931e5b6d26475474f yt/analysis_modules/ppv_cube/ppv_cube.py
--- a/yt/analysis_modules/ppv_cube/ppv_cube.py
+++ b/yt/analysis_modules/ppv_cube/ppv_cube.py
@@ -17,14 +17,6 @@
from yt.visualization.volume_rendering.camera import off_axis_projection
from yt.funcs import get_pbar
-def create_intensity(vmin, vmax, ifield):
- def _intensity(field, data):
- idxs = (data["v_los"] >= vmin) & (data["v_los"] < vmax)
- f = np.zeros(data[ifield].shape)
- f[idxs] = data[ifield][idxs]
- return f
- return _intensity
-
def create_vlos(z_hat):
def _v_los(field, data):
vz = data["velocity_x"]*z_hat[0] + \
@@ -90,9 +82,11 @@
self.v_bnd = -vmax, vmax
else:
self.v_bnd = (ds.quan(velocity_bounds[0], velocity_bounds[2]),
- ds.quan(velocity_bounds[1], velocity_bounds[2]))
+ ds.quan(velocity_bounds[1], velocity_bounds[2]))
- vbins = np.linspace(self.v_bnd[0], self.v_bnd[1], num=self.nv+1)
+ self.vbins = np.linspace(self.v_bnd[0], self.v_bnd[1], num=self.nv+1)
+ self.vmid = 0.5*(self.vbins[1:]+self.vbins[:-1])
+ self.dv = (self.v_bnd[1]-self.v_bnd[0])/self.nv
_vlos = create_vlos(orient.unit_vectors[2])
ds.field_info.add_field(("gas","v_los"), function=_vlos, units="cm/s")
@@ -100,11 +94,8 @@
self.data = ds.arr(np.zeros((self.nx,self.ny,self.nv)), self.field_units)
pbar = get_pbar("Generating cube.", self.nv)
for i in xrange(self.nv):
- v1 = vbins[i]
- v2 = vbins[i+1]
- _intensity = create_intensity(v1, v2, field)
- ds.field_info.add_field(("gas","intensity"),
- function=_intensity, units=self.field_units)
+ _intensity = self._create_intensity(i)
+ ds.add_field(("gas","intensity"), function=_intensity, units=self.field_units)
prj = off_axis_projection(ds, ds.domain_center, normal, width,
(self.nx, self.ny), "intensity")
self.data[:,:,i] = prj[:,:]
@@ -145,7 +136,7 @@
dx = length_unit[0]/self.nx
dy = length_unit[0]/self.ny
- dv = (self.v_bnd[1]-self.v_bnd[0]).in_units("m/s").value/self.nv
+ dv = self.dv.in_units("m/s").value
if length_unit[1] == "deg":
dx *= -1.
@@ -162,3 +153,11 @@
fib[0].header["btype"] = self.field
fib.writeto(filename, clobber=clobber)
+
+ def _create_intensity(self, i):
+ def _intensity(field, data):
+ w = np.abs(data["v_los"]-self.vmid[i])/self.dv
+ w = 1.-w
+ w[w < 0.0] = 0.0
+ return data[self.field]*w
+ return _intensity
diff -r 3c7983a318d58fcd39b65eaf24198a3d03e0cb19 -r aef63614854a28effe3680c931e5b6d26475474f yt/frontends/fits/data_structures.py
--- a/yt/frontends/fits/data_structures.py
+++ b/yt/frontends/fits/data_structures.py
@@ -49,9 +49,9 @@
regex_pattern = '|'.join(re.escape(_) for _ in delimiters)
spec_names = {"V":"Velocity",
- "FREQ":"Frequency",
- "ENER":"Energy",
- "WAV":"Wavelength"}
+ "F":"Frequency",
+ "E":"Energy",
+ "W":"Wavelength"}
field_from_unit = {"Jy":"intensity",
"K":"temperature"}
Repository URL: https://bitbucket.org/yt_analysis/yt/
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