[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Wed Apr 6 11:09:56 PDT 2016
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/81dc5b3d5633/
Changeset: 81dc5b3d5633
Branch: yt
User: ngoldbaum
Date: 2016-03-31 02:52:12+00:00
Summary: logging: don't create a StreamHandler unless we will use it. Closes #1024
Affected #: 1 file
diff -r ac130eab01032636d00b9de431b8e5f1b4b788d6 -r 81dc5b3d563331842988e4a09e42232e833ddb14 yt/utilities/logger.py
--- a/yt/utilities/logger.py
+++ b/yt/utilities/logger.py
@@ -54,36 +54,43 @@
ytLogger = logging.getLogger("yt")
-yt_sh = logging.StreamHandler(stream=stream)
-# create formatter and add it to the handlers
-formatter = logging.Formatter(ufstring)
-yt_sh.setFormatter(formatter)
-# add the handler to the logger
-ytLogger.addHandler(yt_sh)
-ytLogger.setLevel(level)
-ytLogger.propagate = False
-
def disable_stream_logging():
- ytLogger.removeHandler(ytLogger.handlers[0])
+ if len(ytLogger.handlers) > 0:
+ ytLogger.removeHandler(ytLogger.handlers[0])
h = logging.NullHandler()
ytLogger.addHandler(h)
-original_emitter = yt_sh.emit
-
def colorize_logging():
f = logging.Formatter(cfstring)
ytLogger.handlers[0].setFormatter(f)
yt_sh.emit = add_coloring_to_emit_ansi(yt_sh.emit)
def uncolorize_logging():
- f = logging.Formatter(ufstring)
- ytLogger.handlers[0].setFormatter(f)
- yt_sh.emit = original_emitter
-
-if ytcfg.getboolean("yt", "coloredlogs"):
- colorize_logging()
+ try:
+ f = logging.Formatter(ufstring)
+ ytLogger.handlers[0].setFormatter(f)
+ yt_sh.emit = original_emitter
+ except NameError:
+ # yt_sh and original_emitter are not defined because
+ # suppressStreamLogging is True, so we continue since there is nothing
+ # to uncolorize
+ pass
if ytcfg.getboolean("yt", "suppressStreamLogging"):
disable_stream_logging()
+else:
+ yt_sh = logging.StreamHandler(stream=stream)
+ # create formatter and add it to the handlers
+ formatter = logging.Formatter(ufstring)
+ yt_sh.setFormatter(formatter)
+ # add the handler to the logger
+ ytLogger.addHandler(yt_sh)
+ ytLogger.setLevel(level)
+ ytLogger.propagate = False
+
+ original_emitter = yt_sh.emit
+
+ if ytcfg.getboolean("yt", "coloredlogs"):
+ colorize_logging()
ytLogger.debug("Set log level to %s", level)
https://bitbucket.org/yt_analysis/yt/commits/def617b415de/
Changeset: def617b415de
Branch: yt
User: ngoldbaum
Date: 2016-03-31 14:43:16+00:00
Summary: Merging with mainline
Affected #: 14 files
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 doc/source/analyzing/mesh_filter.ipynb
--- a/doc/source/analyzing/mesh_filter.ipynb
+++ b/doc/source/analyzing/mesh_filter.ipynb
@@ -143,13 +143,13 @@
"source": [
"ph1 = yt.PhasePlot(ad, 'density', 'temperature', 'cell_mass', weight_field=None)\n",
"ph1.set_xlim(3e-31, 3e-27)\n",
- "ph1.set_title('cell_mass', 'No Cuts')\n",
+ "ph1.annotate_title('No Cuts')\n",
"ph1.set_figure_size(5)\n",
"ph1.show()\n",
"\n",
"ph1 = yt.PhasePlot(dense_ad, 'density', 'temperature', 'cell_mass', weight_field=None)\n",
"ph1.set_xlim(3e-31, 3e-27)\n",
- "ph1.set_title('cell_mass', 'Dense Gas')\n",
+ "ph1.annotate_title('Dense Gas')\n",
"ph1.set_figure_size(5)\n",
"ph1.show()"
]
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 doc/source/cookbook/tests/test_cookbook.py
--- a/doc/source/cookbook/tests/test_cookbook.py
+++ b/doc/source/cookbook/tests/test_cookbook.py
@@ -11,16 +11,22 @@
"""
import glob
import os
+import sys
import subprocess
PARALLEL_TEST = {"rockstar_nest.py": "3"}
+BLACKLIST = ["opengl_ipython.py", "opengl_vr.py"]
+if sys.version_info >= (3,0,0):
+ BLACKLIST.append("rockstar_nest.py")
def test_recipe():
'''Dummy test grabbing all cookbook's recipes'''
for fname in glob.glob("doc/source/cookbook/*.py"):
recipe = os.path.basename(fname)
+ if recipe in BLACKLIST:
+ continue
check_recipe.description = "Testing recipe: %s" % recipe
if recipe in PARALLEL_TEST:
yield check_recipe, \
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 doc/source/reference/api/api.rst
--- a/doc/source/reference/api/api.rst
+++ b/doc/source/reference/api/api.rst
@@ -743,6 +743,7 @@
~yt.visualization.plot_window.PWViewerMPL.annotate_clear
~yt.visualization.plot_modifications.ArrowCallback
+ ~yt.visualization.plot_modifications.CellEdgesCallback
~yt.visualization.plot_modifications.ClumpContourCallback
~yt.visualization.plot_modifications.ContourCallback
~yt.visualization.plot_modifications.CuttingQuiverCallback
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 doc/source/visualizing/callbacks.rst
--- a/doc/source/visualizing/callbacks.rst
+++ b/doc/source/visualizing/callbacks.rst
@@ -273,6 +273,31 @@
slc.annotate_grids()
slc.save()
+.. _annotate-cell-edges:
+
+Overplot Cell Edges
+~~~~~~~~~~~~~~~~~~~
+
+.. function:: annotate_cell_edges(line_width=1.0, alpha = 1.0,
+ color = (0.0, 0.0, 0.0))
+
+ (This is a proxy for
+ :class:`~yt.visualization.plot_modifications.CellEdgesCallback`.)
+
+ Annotate the edges of cells, where the ``line_width`` in pixels is specified.
+ The ``alpha`` of the overlaid image and the ``color`` of the lines are also
+ specifiable. Note that because the lines are drawn from both sides of a
+ cell, the image sometimes has the effect of doubling the line width.
+ Color here is in RGB float values (0 to 1).
+
+.. python-script::
+
+ import yt
+ ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
+ slc = yt.SlicePlot(ds, 'z', 'density', width=(10,'kpc'), center='max')
+ slc.annotate_cell_edges()
+ slc.save()
+
.. _annotate-halos:
Overplot Halo Annotations
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 tests/tests_2.7.yaml
--- a/tests/tests_2.7.yaml
+++ b/tests/tests_2.7.yaml
@@ -42,7 +42,7 @@
local_tipsy_270:
- yt/frontends/tipsy/tests/test_outputs.py
- local_varia_273:
+ local_varia_274:
- yt/analysis_modules/radmc3d_export
- yt/frontends/moab/tests/test_c5.py
- yt/analysis_modules/photon_simulator/tests/test_spectra.py
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 tests/tests_3.5.yaml
--- a/tests/tests_3.5.yaml
+++ b/tests/tests_3.5.yaml
@@ -25,6 +25,8 @@
local_halos_350:
- yt/frontends/owls_subfind/tests/test_outputs.py
+ - yt/frontends/gadget_fof/tests/test_outputs.py:test_fields_g5
+ - yt/frontends/gadget_fof/tests/test_outputs.py:test_fields_g42
local_owls_350:
- yt/frontends/owls/tests/test_outputs.py
@@ -40,7 +42,7 @@
local_tipsy_350:
- yt/frontends/tipsy/tests/test_outputs.py
- local_varia_350:
+ local_varia_351:
- yt/analysis_modules/radmc3d_export
- yt/frontends/moab/tests/test_c5.py
- yt/analysis_modules/photon_simulator/tests/test_spectra.py
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/frontends/gadget_fof/tests/test_outputs.py
--- a/yt/frontends/gadget_fof/tests/test_outputs.py
+++ b/yt/frontends/gadget_fof/tests/test_outputs.py
@@ -62,7 +62,7 @@
for hid in range(0, ds.index.particle_count["Group"]):
my_h = ds.halo("Group", hid)
h_ids = my_h["ID"]
- for sid in range(my_h["subhalo_number"]):
+ for sid in range(int(my_h["subhalo_number"][0])):
my_s = ds.halo("Subhalo", (my_h.particle_identifier, sid))
total_sub += my_s["ID"].size
total_int += np.intersect1d(h_ids, my_s["ID"]).size
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -31,6 +31,8 @@
from cython.parallel import prange, parallel, threadid
from vec3_ops cimport dot, subtract, L2_norm, fma
+from cpython.exc cimport PyErr_CheckSignals
+
DEF Nch = 4
cdef class PartitionedGrid:
@@ -458,6 +460,7 @@
size = nx * ny
cdef ImageAccumulator *idata
cdef np.float64_t width[3]
+ cdef int chunksize = 100
for i in range(3):
width[i] = self.width[i]
with nogil, parallel(num_threads = num_threads):
@@ -465,7 +468,7 @@
idata.supp_data = self.supp_data
v_pos = <np.float64_t *> malloc(3 * sizeof(np.float64_t))
v_dir = <np.float64_t *> malloc(3 * sizeof(np.float64_t))
- for j in prange(size, schedule="static", chunksize=100):
+ for j in prange(size, schedule="static", chunksize=chunksize):
vj = j % ny
vi = (j - vj) / ny + iter[0]
vj = vj + iter[2]
@@ -476,6 +479,9 @@
max_t = fclip(im.zbuffer[vi, vj], 0.0, 1.0)
walk_volume(vc, v_pos, v_dir, self.sampler,
(<void *> idata), NULL, max_t)
+ if (j % (10*chunksize)) == 0:
+ with gil:
+ PyErr_CheckSignals()
for i in range(Nch):
im.image[vi, vj, i] = idata.rgba[i]
free(idata)
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/utilities/lib/pixelization_routines.pyx
--- a/yt/utilities/lib/pixelization_routines.pyx
+++ b/yt/utilities/lib/pixelization_routines.pyx
@@ -61,10 +61,12 @@
int cols, int rows, bounds,
int antialias = 1,
period = None,
- int check_period = 1):
+ int check_period = 1,
+ np.float64_t line_width = 0.0):
cdef np.float64_t x_min, x_max, y_min, y_max
cdef np.float64_t period_x = 0.0, period_y = 0.0
cdef np.float64_t width, height, px_dx, px_dy, ipx_dx, ipx_dy
+ cdef np.float64_t ld_x, ld_y, cx, cy
cdef int i, j, p, xi, yi
cdef int lc, lr, rc, rr
cdef np.float64_t lypx, rypx, lxpx, rxpx, overlap1, overlap2
@@ -170,13 +172,29 @@
for j in range(lc, rc):
lxpx = px_dx * j + x_min
rxpx = px_dx * (j+1) + x_min
- if antialias == 1:
+ if line_width > 0:
+ # Here, we figure out if we're within
+ # line_width*px_dx of the cell edge
+ # Midpoint of x:
+ cx = (rxpx+lxpx)*0.5
+ ld_x = fmin(fabs(cx - (xsp+dxsp)),
+ fabs(cx - (xsp-dxsp)))
+ ld_x *= ipx_dx
+ # Midpoint of y:
+ cy = (rypx+lypx)*0.5
+ ld_y = fmin(fabs(cy - (ysp+dysp)),
+ fabs(cy - (ysp-dysp)))
+ ld_y *= ipx_dy
+ if ld_x <= line_width or ld_y <= line_width:
+ my_array[j,i] = 1.0
+ elif antialias == 1:
overlap1 = ((fmin(rxpx, xsp+dxsp)
- fmax(lxpx, (xsp-dxsp)))*ipx_dx)
if overlap1 < 0.0: continue
my_array[j,i] += (dsp * overlap1) * overlap2
else:
my_array[j,i] = dsp
+
return my_array
@cython.cdivision(True)
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -36,7 +36,8 @@
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, pixelize_off_axis_cartesian
+ pixelize_element_mesh, pixelize_off_axis_cartesian, \
+ pixelize_cartesian
from yt.analysis_modules.cosmological_observation.light_ray.light_ray import \
periodic_ray
from yt.utilities.lib.line_integral_convolution import \
@@ -2361,3 +2362,68 @@
plot._axes.hold(False)
return plot
+
+class CellEdgesCallback(PlotCallback):
+ """
+ annotate_cell_edges(line_width=1.0, alpha = 1.0, color = (0.0, 0.0, 0.0))
+
+ Annotate cell edges. This is done through a second call to pixelize, where
+ the distance from a pixel to a cell boundary in pixels is compared against
+ the `line_width` argument. The secondary image is colored as `color` and
+ overlaid with the `alpha` value.
+
+ Parameters
+ ----------
+ line_width : float
+ Distance, in pixels, from a cell edge that will mark a pixel as being
+ annotated as a cell edge. Default is 1.0.
+ alpha : float
+ When the second image is overlaid, it will have this level of alpha
+ transparency. Default is 1.0 (fully-opaque).
+ color : tuple of three floats
+ This is the color of the cell edge values. It defaults to black.
+
+ Examples
+ --------
+
+ >>> import yt
+ >>> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
+ >>> s = yt.SlicePlot(ds, 'z', 'density')
+ >>> s.annotate_cell_edges()
+ >>> s.save()
+ """
+ _type_name = "cell_edges"
+ def __init__(self, line_width=1.0, alpha = 1.0, color=(0.0, 0.0, 0.0)):
+ PlotCallback.__init__(self)
+ self.line_width = line_width
+ self.alpha = alpha
+ self.color = (np.array(color) * 255).astype("uint8")
+
+ def __call__(self, plot):
+ x0, x1 = plot.xlim
+ y0, y1 = plot.ylim
+ xx0, xx1 = plot._axes.get_xlim()
+ yy0, yy1 = plot._axes.get_ylim()
+ plot._axes.hold(True)
+ nx = plot.image._A.shape[0]
+ ny = plot.image._A.shape[1]
+ im = pixelize_cartesian(plot.data['px'],
+ plot.data['py'],
+ plot.data['pdx'],
+ plot.data['pdy'],
+ plot.data['px'], # dummy field
+ int(nx), int(ny),
+ (x0, x1, y0, y1),
+ line_width=self.line_width).transpose()
+ # New image:
+ im_buffer = np.zeros((nx, ny, 4), dtype="uint8")
+ im_buffer[im>0,3] = 255
+ im_buffer[im>0,:3] = self.color
+ plot._axes.imshow(im_buffer, origin='lower',
+ interpolation='nearest',
+ extent = [xx0, xx1, yy0, yy1],
+ alpha = self.alpha)
+ plot._axes.set_xlim(xx0,xx1)
+ plot._axes.set_ylim(yy0,yy1)
+ plot._axes.hold(False)
+
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/visualization/profile_plotter.py
--- a/yt/visualization/profile_plotter.py
+++ b/yt/visualization/profile_plotter.py
@@ -462,7 +462,7 @@
"""
if field == "all":
self.x_log = log
- for field in self.profiles[0].field_data.keys():
+ for field in list(self.profiles[0].field_data.keys()):
self.y_log[field] = log
else:
field, = self.profiles[0].data_source._determine_fields([field])
@@ -578,7 +578,7 @@
"""
if field is 'all':
- fields = self.axes.keys()
+ fields = list(self.axes.keys())
else:
fields = ensure_list(field)
for profile in self.profiles:
@@ -697,7 +697,7 @@
>>> # Change plot properties.
>>> plot.set_cmap("cell_mass", "jet")
>>> plot.set_zlim("cell_mass", 1e8, 1e13)
- >>> plot.set_title("cell_mass", "This is a phase plot")
+ >>> plot.annotate_title("This is a phase plot")
"""
x_log = None
@@ -971,7 +971,7 @@
>>> plot.annotate_text(1e-15, 5e4, "Hello YT")
"""
- for f in self.data_source._determine_fields(self.plots.keys()):
+ for f in self.data_source._determine_fields(list(self.plots.keys())):
if self.plots[f].figure is not None and text is not None:
self.plots[f].axes.text(xpos, ypos, text,
fontproperties=self._font_properties,
@@ -1061,6 +1061,27 @@
return self
@invalidate_plot
+ def annotate_title(self, title):
+ """Set a title for the plot.
+
+ Parameters
+ ----------
+ title : str
+ The title to add.
+
+ Examples
+ --------
+
+ >>> plot.annotate_title("This is a phase plot")
+
+ """
+ for f in self.profile.field_data:
+ if isinstance(f, tuple):
+ f = f[1]
+ self.plot_title[self.data_source._determine_fields(f)[0]] = title
+ return self
+
+ @invalidate_plot
def reset_plot(self):
self.plots = {}
return self
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/visualization/tests/test_callbacks.py
--- a/yt/visualization/tests/test_callbacks.py
+++ b/yt/visualization/tests/test_callbacks.py
@@ -341,6 +341,25 @@
max_level=3, cmap="gist_stern")
p.save(prefix)
+def test_cell_edges_callback():
+ with _cleanup_fname() as prefix:
+ ds = fake_amr_ds(fields = ("density",))
+ for ax in 'xyz':
+ p = ProjectionPlot(ds, ax, "density")
+ p.annotate_cell_edges()
+ yield assert_fname, p.save(prefix)[0]
+ p = ProjectionPlot(ds, ax, "density", weight_field="density")
+ p.annotate_cell_edges()
+ yield assert_fname, p.save(prefix)[0]
+ p = SlicePlot(ds, ax, "density")
+ p.annotate_cell_edges()
+ yield assert_fname, p.save(prefix)[0]
+ # Now we'll check a few additional minor things
+ p = SlicePlot(ds, "x", "density")
+ p.annotate_cell_edges(alpha=0.7, line_width=0.9,
+ color=(0.0, 1.0, 1.0))
+ p.save(prefix)
+
def test_line_integral_convolution_callback():
with _cleanup_fname() as prefix:
ds = fake_amr_ds(fields =
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/visualization/volume_rendering/lens.py
--- a/yt/visualization/volume_rendering/lens.py
+++ b/yt/visualization/volume_rendering/lens.py
@@ -277,8 +277,8 @@
dz = np.dot(pos - position, camera.unit_vectors[2])
# Transpose into image coords.
- px = (res[0] * 0.5 + res[0] / camera.width[0].d * dx).astype('int')
- py = (res[1] * 0.5 + res[1] / camera.width[1].d * dy).astype('int')
+ px = (res[0] * 0.5 + res[0] / width[0] * dx).astype('int64')
+ py = (res[1] * 0.5 + res[1] / width[1] * dy).astype('int64')
return px, py, dz
diff -r 81dc5b3d563331842988e4a09e42232e833ddb14 -r def617b415dec95ac24052fd0d378a3700fcd092 yt/visualization/volume_rendering/tests/test_mesh_render.py
--- a/yt/visualization/volume_rendering/tests/test_mesh_render.py
+++ b/yt/visualization/volume_rendering/tests/test_mesh_render.py
@@ -52,6 +52,7 @@
def mesh_render_image_func(filename_prefix):
return im.write_image(filename_prefix)
+ mesh_render_image_func.__name__ = "func_{}".format(test_prefix)
test = GenericImageTest(ds, mesh_render_image_func, decimals)
test.prefix = test_prefix
return test
https://bitbucket.org/yt_analysis/yt/commits/c55b7a1e36bf/
Changeset: c55b7a1e36bf
Branch: yt
User: jzuhone
Date: 2016-04-06 18:09:47+00:00
Summary: Merged in ngoldbaum/yt (pull request #2102)
logging: don't create a StreamHandler unless we will use it. Closes #1024
Affected #: 1 file
diff -r 068a53069cdff7da3ad9597a7bb868fcafabecb2 -r c55b7a1e36bf638dffa73074a047cc5c2e245bf7 yt/utilities/logger.py
--- a/yt/utilities/logger.py
+++ b/yt/utilities/logger.py
@@ -54,36 +54,43 @@
ytLogger = logging.getLogger("yt")
-yt_sh = logging.StreamHandler(stream=stream)
-# create formatter and add it to the handlers
-formatter = logging.Formatter(ufstring)
-yt_sh.setFormatter(formatter)
-# add the handler to the logger
-ytLogger.addHandler(yt_sh)
-ytLogger.setLevel(level)
-ytLogger.propagate = False
-
def disable_stream_logging():
- ytLogger.removeHandler(ytLogger.handlers[0])
+ if len(ytLogger.handlers) > 0:
+ ytLogger.removeHandler(ytLogger.handlers[0])
h = logging.NullHandler()
ytLogger.addHandler(h)
-original_emitter = yt_sh.emit
-
def colorize_logging():
f = logging.Formatter(cfstring)
ytLogger.handlers[0].setFormatter(f)
yt_sh.emit = add_coloring_to_emit_ansi(yt_sh.emit)
def uncolorize_logging():
- f = logging.Formatter(ufstring)
- ytLogger.handlers[0].setFormatter(f)
- yt_sh.emit = original_emitter
-
-if ytcfg.getboolean("yt", "coloredlogs"):
- colorize_logging()
+ try:
+ f = logging.Formatter(ufstring)
+ ytLogger.handlers[0].setFormatter(f)
+ yt_sh.emit = original_emitter
+ except NameError:
+ # yt_sh and original_emitter are not defined because
+ # suppressStreamLogging is True, so we continue since there is nothing
+ # to uncolorize
+ pass
if ytcfg.getboolean("yt", "suppressStreamLogging"):
disable_stream_logging()
+else:
+ yt_sh = logging.StreamHandler(stream=stream)
+ # create formatter and add it to the handlers
+ formatter = logging.Formatter(ufstring)
+ yt_sh.setFormatter(formatter)
+ # add the handler to the logger
+ ytLogger.addHandler(yt_sh)
+ ytLogger.setLevel(level)
+ ytLogger.propagate = False
+
+ original_emitter = yt_sh.emit
+
+ if ytcfg.getboolean("yt", "coloredlogs"):
+ colorize_logging()
ytLogger.debug("Set log level to %s", level)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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