[yt-svn] commit/yt: ngoldbaum: Merged in MatthewTurk/yt (pull request #1959)
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commits-noreply at bitbucket.org
Wed Jan 27 09:13:44 PST 2016
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/29b4b633e951/
Changeset: 29b4b633e951
Branch: yt
User: ngoldbaum
Date: 2016-01-27 17:13:36+00:00
Summary: Merged in MatthewTurk/yt (pull request #1959)
Rewrite off-axis pixelization in Cython
Affected #: 4 files
diff -r 7b3234d68c60aa8d575160408559fbc03089b058 -r 29b4b633e95188794e985934b7d3cfe2d158ad78 yt/geometry/coordinates/cartesian_coordinates.py
--- a/yt/geometry/coordinates/cartesian_coordinates.py
+++ b/yt/geometry/coordinates/cartesian_coordinates.py
@@ -23,7 +23,7 @@
cylindrical_to_cartesian
from yt.funcs import mylog
from yt.utilities.lib.pixelization_routines import \
- pixelize_element_mesh
+ pixelize_element_mesh, pixelize_off_axis_cartesian
from yt.data_objects.unstructured_mesh import SemiStructuredMesh
import yt.visualization._MPL as _MPL
@@ -134,7 +134,8 @@
def _oblique_pixelize(self, data_source, field, bounds, size, antialias):
indices = np.argsort(data_source['dx'])[::-1]
- buff = _MPL.CPixelize(data_source['x'], data_source['y'],
+ buff = pixelize_off_axis_cartesian(
+ data_source['x'], data_source['y'],
data_source['z'], data_source['px'],
data_source['py'], data_source['pdx'],
data_source['pdy'], data_source['pdz'],
diff -r 7b3234d68c60aa8d575160408559fbc03089b058 -r 29b4b633e95188794e985934b7d3cfe2d158ad78 yt/utilities/lib/pixelization_routines.pyx
--- a/yt/utilities/lib/pixelization_routines.pyx
+++ b/yt/utilities/lib/pixelization_routines.pyx
@@ -178,6 +178,93 @@
my_array[j,i] = dsp
return my_array
+ at cython.cdivision(True)
+ at cython.boundscheck(False)
+ at cython.wraparound(False)
+def pixelize_off_axis_cartesian(
+ np.float64_t[:] x,
+ np.float64_t[:] y,
+ np.float64_t[:] z,
+ np.float64_t[:] px,
+ np.float64_t[:] py,
+ np.float64_t[:] pdx,
+ np.float64_t[:] pdy,
+ np.float64_t[:] pdz,
+ np.float64_t[:] center,
+ np.float64_t[:,:] inv_mat,
+ np.int64_t[:] indices,
+ np.float64_t[:] data,
+ int cols, int rows, bounds):
+ cdef np.float64_t x_min, x_max, y_min, y_max
+ cdef np.float64_t width, height, px_dx, px_dy, ipx_dx, ipx_dy, md
+ cdef int i, j, p, ip
+ cdef int lc, lr, rc, rr
+ # These are the temp vars we get from the arrays
+ cdef np.float64_t xsp, ysp, zsp, dxsp, dysp, dzsp, dsp
+ cdef np.float64_t pxsp, pysp, cxpx, cypx, cx, cy, cz
+ # Some periodicity helpers
+ cdef np.ndarray[np.float64_t, ndim=2] my_array
+ cdef np.ndarray[np.int64_t, ndim=2] mask
+ x_min = bounds[0]
+ x_max = bounds[1]
+ y_min = bounds[2]
+ y_max = bounds[3]
+ width = x_max - x_min
+ height = y_max - y_min
+ px_dx = width / (<np.float64_t> rows)
+ px_dy = height / (<np.float64_t> cols)
+ ipx_dx = 1.0 / px_dx
+ ipx_dy = 1.0 / px_dy
+ if rows == 0 or cols == 0:
+ raise YTPixelizeError("Cannot scale to zero size")
+ if px.shape[0] != py.shape[0] or \
+ px.shape[0] != pdx.shape[0] or \
+ px.shape[0] != pdy.shape[0] or \
+ px.shape[0] != pdz.shape[0] or \
+ px.shape[0] != indices.shape[0] or \
+ px.shape[0] != data.shape[0]:
+ raise YTPixelizeError("Arrays are not of correct shape.")
+ my_array = np.zeros((rows, cols), "float64")
+ mask = np.zeros((rows, cols), "int64")
+ with nogil:
+ for ip in range(indices.shape[0]):
+ p = indices[ip]
+ xsp = x[p]
+ ysp = y[p]
+ zsp = z[p]
+ pxsp = px[p]
+ pysp = py[p]
+ dxsp = pdx[p]
+ dysp = pdy[p]
+ dzsp = pdz[p]
+ dsp = data[p]
+ # Any point we want to plot is at most this far from the center
+ md = 2.0 * math.sqrt(dxsp*dxsp + dysp*dysp + dzsp*dzsp)
+ if pxsp + md < x_min or \
+ pxsp - md > x_max or \
+ pysp + md < y_min or \
+ pysp - md > y_max:
+ continue
+ lc = <int> fmax(((pxsp - md - x_min)*ipx_dx),0)
+ lr = <int> fmax(((pysp - md - y_min)*ipx_dy),0)
+ rc = <int> fmin(((pxsp + md - x_min)*ipx_dx + 1), rows)
+ rr = <int> fmin(((pysp + md - y_min)*ipx_dy + 1), cols)
+ for i in range(lr, rr):
+ cypx = px_dy * (i + 0.5) + y_min
+ for j in range(lc, rc):
+ cxpx = px_dx * (j + 0.5) + x_min
+ cx = inv_mat[0,0]*cxpx + inv_mat[0,1]*cypx + center[0]
+ cy = inv_mat[1,0]*cxpx + inv_mat[1,1]*cypx + center[1]
+ cz = inv_mat[2,0]*cxpx + inv_mat[2,1]*cypx + center[2]
+ if fabs(xsp - cx) * 0.95 > dxsp or \
+ fabs(ysp - cy) * 0.95 > dysp or \
+ fabs(zsp - cz) * 0.95 > dzsp:
+ continue
+ mask[i, j] = 1
+ my_array[i, j] += dsp
+ my_array /= mask
+ return my_array
+
@cython.cdivision(True)
@cython.boundscheck(False)
diff -r 7b3234d68c60aa8d575160408559fbc03089b058 -r 29b4b633e95188794e985934b7d3cfe2d158ad78 yt/visualization/fixed_resolution.py
--- a/yt/visualization/fixed_resolution.py
+++ b/yt/visualization/fixed_resolution.py
@@ -23,11 +23,10 @@
from .fixed_resolution_filters import apply_filter, filter_registry
from yt.data_objects.image_array import ImageArray
from yt.utilities.lib.pixelization_routines import \
- pixelize_cylinder
+ pixelize_cylinder, pixelize_off_axis_cartesian
from yt.utilities.lib.api import add_points_to_greyscale_image
from yt.frontends.stream.api import load_uniform_grid
-from . import _MPL
import numpy as np
import weakref
import re
@@ -537,7 +536,8 @@
if hasattr(b, "in_units"):
b = float(b.in_units("code_length"))
bounds.append(b)
- buff = _MPL.CPixelize( self.data_source['x'], self.data_source['y'], self.data_source['z'],
+ buff = pixelize_off_axis_cartesian(
+ self.data_source['x'], self.data_source['y'], self.data_source['z'],
self.data_source['px'], self.data_source['py'],
self.data_source['pdx'], self.data_source['pdy'], self.data_source['pdz'],
self.data_source.center, self.data_source._inv_mat, indices,
diff -r 7b3234d68c60aa8d575160408559fbc03089b058 -r 29b4b633e95188794e985934b7d3cfe2d158ad78 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -33,7 +33,8 @@
from yt.units.yt_array import YTQuantity, YTArray
from yt.visualization.image_writer import apply_colormap
from yt.utilities.lib.geometry_utils import triangle_plane_intersect
-from yt.utilities.lib.pixelization_routines import pixelize_element_mesh
+from yt.utilities.lib.pixelization_routines import \
+ pixelize_element_mesh, pixelize_off_axis_cartesian
from yt.analysis_modules.cosmological_observation.light_ray.light_ray import \
periodic_ray
from yt.utilities.lib.line_integral_convolution import \
@@ -829,14 +830,16 @@
nx = plot.image._A.shape[0] / self.factor
ny = plot.image._A.shape[1] / self.factor
indices = np.argsort(plot.data['dx'])[::-1]
- pixX = _MPL.CPixelize( plot.data['x'], plot.data['y'], plot.data['z'],
+ pixX = pixelize_off_axis_cartesian(
+ plot.data['x'], plot.data['y'], plot.data['z'],
plot.data['px'], plot.data['py'],
plot.data['pdx'], plot.data['pdy'], plot.data['pdz'],
plot.data.center, plot.data._inv_mat, indices,
plot.data[self.field_x],
int(nx), int(ny),
(x0, x1, y0, y1),).transpose()
- pixY = _MPL.CPixelize( plot.data['x'], plot.data['y'], plot.data['z'],
+ pixY = pixelize_off_axis_cartesian(
+ plot.data['x'], plot.data['y'], plot.data['z'],
plot.data['px'], plot.data['py'],
plot.data['pdx'], plot.data['pdy'], plot.data['pdz'],
plot.data.center, plot.data._inv_mat, indices,
Repository URL: https://bitbucket.org/yt_analysis/yt/
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