[yt-users] python 3, yet another demo fail + fix

27 Aug 2015

      Dear Nathan,

there is also a fail in 6)_Volume_Rendering, 2nd cell, from the 
cam.show() call that is related:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-2-978925a24bd8> in <module>()
       2 tf.add_layers(4, w=0.01)
       3 cam = ds.camera([0.5, 0.5, 0.5], [1.0, 1.0, 1.0], (20, 'kpc'), 
512, tf, fields=["density"])
----> 4 cam.show()

/home/alex/Python/lib/python3.4/site-packages/yt/visualization/volume_rendering/camera.py 
in show(self, clip_ratio)
     801             image = self.snapshot()[:,:,:3]
     802             if clip_ratio is not None: clip_ratio *= image.std()
--> 803             data = write_bitmap(image, None, clip_ratio)
     804             publish_display_data(
     805                 data={'image/png': data},

/home/alex/Python/lib/python3.4/site-packages/yt/visualization/image_writer.py 
in write_bitmap(bitmap_array, filename, max_val, transpose)
     175         pw.write_png(bitmap_array, filename)
     176     else:
--> 177         return pw.write_png_to_string(bitmap_array.copy())
     178     return bitmap_array
     179

/home/alex/Python/lib/python3.4/site-packages/yt/utilities/png_writer.py 
in write_png_to_string(buffer, dpi, gray)
      30     fileobj = IO()
      31 #    _png.write_png(buffer, width, height, fileobj, dpi)
---> 32     _png.write_png(buffer, fileobj, dpi)
      33     png_str = fileobj.getvalue()
      34     fileobj.close()

TypeError: string argument expected, got 'bytes'

----------------------

this has to do with strings in python3 are no longer used for buffers 
but the bytes type.
yt/utilities/png_writer.py

attached I send you a fixed version (you may want to remove the "#-" 
commended line I left in from the previous version.  This now fixes this 
and the previous bug (below).

hopefully this is all I need to fix for now, otherwise I probably should 
start using your development framework to submit fixes / pull requests.

Best wishes,
Alexander

On 27/08/15 20:54, Alexander Heger wrote:
...
Dear Nathan,
I now ran further through the demo and this time I got stuck in
4)_Data_Objects_and_Time_Series
in section "Slice Queries", 3rd input field, the line
yt.write_image(np.log10(frb["gas", "density"]), "temp.png")
causes a trace back
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-17-6cc738ba1725> in <module>()
----> 1 yt.write_image(np.log10(frb["gas", "density"]), "temp.png")
       2 #from IPython.display import Image
       3 #Image(filename = "temp.png")
/home/alex/Python/lib/python3.4/site-packages/yt/visualization/image_writer.py
in write_image(image, filename, color_bounds, cmap_name, func)
     217         image = image[:,:,0]
     218     to_plot = apply_colormap(image, color_bounds =
color_bounds, cmap_name = cmap_name)
--> 219     pw.write_png(to_plot, filename)
     220     return to_plot
     221
/home/alex/Python/lib/python3.4/site-packages/yt/utilities/png_writer.py
in write_png(buffer, filename, dpi)
      17     width = buffer.shape[1]
      18     height = buffer.shape[0]
---> 19     _png.write_png(buffer, width, height, filename, dpi)
      20
      21 def write_png_to_string(buffer, dpi=100, gray=0):
TypeError: write_png() takes at most 3 arguments (5 given)
----------------------------
I think I have seen this error in yt version 3.0 or 3.1 before.
(still using current 3.2)
What seems to fix this for me is to change yt/utilities/png_writer.py
def write_png(buffer, filename, dpi=100):
#    width = buffer.shape[1]
#    height = buffer.shape[0]
#    _png.write_png(buffer, width, height, filename, dpi)
     _png.write_png(buffer, filename, dpi)
def write_png_to_string(buffer, dpi=100, gray=0):
#    width = buffer.shape[1]
#    height = buffer.shape[0]
     fileobj = cStringIO()
#    _png.write_png(buffer, width, height, fileobj, dpi)
     _png.write_png(buffer, fileobj, dpi)
     png_str = fileobj.getvalue()
     fileobj.close()
     return png_str
(note:
In [1]: mpl.__version__
Out[1]: '1.5.dev1'
)
At this point, to get/keep these fixes I probably should switch to the
development version of yt?
Best wishes,
Alexander
On 27/08/15 17:46, Alexander Heger wrote:
...
Dear Nathan,
I now switched to the current matplotlibrc files and with that it seems
to work.
Thanks a lot.
As another question: is ok or ill-advised to run with the current yt
development version instead of the latest release?
Best wishes,
Alexander
On 27/08/15 00:26, Nathan Goldbaum wrote:
...
On Wed, Aug 26, 2015 at 4:48 AM, Alexander Heger mailto:alex.heger@gmail.com> wrote:
Dear Nathan,
Thanks for the report about this, we should make the quickstart
        notebooks work under both python 2 and python 3.  I've filed an
        issue to
        track this here:
https://bitbucket.org/yt_analysis/yt/issues/1073/quickstart-notebooks-do-not...
Python 3 is still new to yt, so there are rough edges that
you're
        running across. It really helps to get reports back from python3
        users,
        especially new users where things are confusing in yt. So
thank you!
I ma happy to help, it is my interest to get it run - I use and
    teach students to use python 3 since there is many cool new features
    in py3.
I'm not sure what's up with the font issue below. I just tried
        running
        the simple visualization notebook under python3 and it worked
on my
        laptop, although that doesn't say much given that we likely
        installed in
        very different ways. The fact that it's looking for cmsy10 is
a bit
        strange since yt doesn't use that font internally. Do you
        perhaps have
        useTex = True somewhere in your matplotlibrc? Even then I'm
        confused why
yes, I would use that; matplotlib seems to work otherwise.
it's crashing since I know many people use that setting
        day-to-day with
        yt and have no issues. I also just tried running that example
        notebook
        using matplotlib's useTex=True setting and it worked.
maybe something is special, I admit that after installation on top
    of my custom-built python 3.4.3 on Fedora 22
cd
    hg clone https://bitbucket.org/yt_analysis/yt
    cd yt
    hg update yt
    pip3 install -r requirements.txt
    pip3 install yt
I upgraded all packages to current version
pip3 freeze --local | grep -v '^\-e' | cut -d = -f 1  | xargs -n1
    pip3 install -U
In either case, it's really a matplotlib issue and there's not
        much we
        can do about it on the yt side. In particular, I don't see any
code
        outside matplotlib in any of your tracebacks. Did you install yt
        using
        the install script, or by "pip install"ing or "conda
        install"ing? Which
        matplotlib version are you running? You can check by doing
"import
        matplotlib; print(matplotlib.__version__)" in the python REPL.
In [1]: mpl.__version__
    Out[1]: '1.4.3'
Maybe I need to check/update my mpl resource file which is not 5 yr
    old...?
I will try to update mpl to current development version
In [1]: mpl.__version__
    Out[1]: '1.5.dev1'
unfortunately the error remains.  I am a bit worried about the line
--> 697             result = self._font[texname.decode('ascii')]
I will check tomorrow where 'cmsy10' may come from.
Should I also be suing the current development version of yt to make
    error tracking against current version (and getting fixes) easier?
(and is this the correct list for this, or should I be using the
    yt-devel list?)
Either list is fine, please also feel free to open an issue, especially
if you can make this error reproducible on another setup.
Best wishes,
    Alexander
-Alexander
---------------------------------------------------------------------------
KeyError                                  Traceback (most
        recent
             call last)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py
        in
             __getitem__(self, texname)
                  706         try:
             --> 707             result = self._font[texname]
                  708         except KeyError:
KeyError: 'cmsy10'
During handling of the above exception, another exception
        occurred:
AttributeError                            Traceback (most
        recent
             call last)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in print_pdf(self, filename, **kwargs)
                 2484
          bbox_inches_restore=_bbox_inches_restore)
             -> 2485             self.figure.draw(renderer)
                 2486             renderer.finalize()
/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py
        in
             draw_wrapper(artist, renderer, *args, **kwargs)
                   58         before(artist, renderer)
             ---> 59         draw(artist, renderer, *args, **kwargs)
                   60         after(artist, renderer)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/figure.py
        in
             draw(self, renderer)
                 1084         for zorder, a, func, args in dsu:
             -> 1085             func(*args)
                 1086
/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py
        in
             draw_wrapper(artist, renderer, *args, **kwargs)
                   58         before(artist, renderer)
             ---> 59         draw(artist, renderer, *args, **kwargs)
                   60         after(artist, renderer)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/axes/_base.py
             in draw(self, renderer, inframe)
                 2109         for zorder, a in dsu:
             -> 2110             a.draw(renderer)
                 2111
/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py
        in
             draw_wrapper(artist, renderer, *args, **kwargs)
                   58         before(artist, renderer)
             ---> 59         draw(artist, renderer, *args, **kwargs)
                   60         after(artist, renderer)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in
             draw(self, renderer, *args, **kwargs)
                 1118         for tick in ticks_to_draw:
             -> 1119             tick.draw(renderer)
                 1120
/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py
        in
             draw_wrapper(artist, renderer, *args, **kwargs)
                   58         before(artist, renderer)
             ---> 59         draw(artist, renderer, *args, **kwargs)
                   60         after(artist, renderer)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/axis.py in
             draw(self, renderer)
                  248         if self.label1On:
             --> 249             self.label1.draw(renderer)
                  250         if self.label2On:
/home/alex/Python/lib/python3.4/site-packages/matplotlib/artist.py
        in
             draw_wrapper(artist, renderer, *args, **kwargs)
                   58         before(artist, renderer)
             ---> 59         draw(artist, renderer, *args, **kwargs)
                   60         after(artist, renderer)
/home/alex/Python/lib/python3.4/site-packages/matplotlib/text.py in
             draw(self, renderer)
                  637                 renderer.draw_tex(gc, x, y,
        clean_line,
             --> 638
          self._fontproperties, angle,
             mtext=mtext)
                  639             else:
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in draw_tex(self, gc, x, y, s, prop, angle, ismath, mtext)
                 1823                 if dvifont.texname not in
             self.file.dviFontInfo:
             -> 1824                     psfont =
             self.tex_font_mapping(dvifont.texname)
                 1825
          self.file.dviFontInfo[dvifont.texname]
             = Bunch(
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in tex_font_mapping(self, texfont)
                 1530
        dviread.PsfontsMap(dviread.find_tex_file('pdftex.map'))
             -> 1531         return self.tex_font_map[texfont]
                 1532
/home/alex/Python/lib/python3.4/site-packages/matplotlib/dviread.py
        in
             __getitem__(self, texname)
                  708         except KeyError:
             --> 709             result =
        self._font[texname.decode('ascii')]
                  710         fn, enc = result.filename, result.encoding
AttributeError: 'str' object has no attribute 'decode'
During handling of the above exception, another exception
        occurred:
FileNotFoundError                         Traceback (most
        recent
             call last)
/home/alex/Python/lib/python3.4/site-packages/IPython/core/formatters.py
             in __call__(self, obj)
                  339             method =
_safe_get_formatter_method(obj,
             self.print_method)
                  340             if method is not None:
             --> 341                 return method()
                  342             return None
                  343         else:
/home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py
in newfunc(*args, **kwargs)
                   75             if hasattr(args[0], 'run_callbacks'):
                   76                 args[0].run_callbacks()
             ---> 77         rv = f(*args, **kwargs)
                   78         return rv
                   79     return newfunc
/home/alex/Python/lib/python3.4/site-packages/yt/visualization/plot_container.py
in _repr_html_(self)
                  642         ret = ''
                  643         for field in self.plots:
             --> 644             img =
             base64.b64encode(self.plots[field]._repr_png_()).decode()
                  645             ret += r'<br>'.format(img)
/home/alex/Python/lib/python3.4/site-packages/yt/visualization/base_plot_types.py
in _repr_png_(self)
                  165         canvas = FigureCanvasAgg(self.figure)
                  166         f = BytesIO()
             --> 167         canvas.print_figure(f)
                  168         f.seek(0)
                  169         return f.read()
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backend_bases.py
in print_figure(self, filename, dpi, facecolor, edgecolor,
             orientation, format, **kwargs)
                 2209                 orientation=orientation,
                 2210
          bbox_inches_restore=_bbox_inches_restore,
             -> 2211                 **kwargs)
                 2212         finally:
                 2213             if bbox_inches and restore_bbox:
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in print_pdf(self, filename, **kwargs)
                 2489                 file.endStream()
                 2490             else:            # we opened the file
        above; now
             finish it off
             -> 2491                 file.close()
                 2492
                 2493
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in close(self)
                  523         self.endStream()
                  524         # Write out the various deferred objects
             --> 525         self.writeFonts()
                  526         self.writeObject(self.alphaStateObject,
                  527                          dict([(val[0], val[1])
/home/alex/Python/lib/python3.4/site-packages/matplotlib/backends/backend_pdf.py
in writeFonts(self)
                  623                 # a normal TrueType font
                  624                 matplotlib.verbose.report('Writing
        TrueType
             font', 'debug')
             --> 625                 realpath, stat_key =
             get_realpath_and_stat(filename)
                  626                 chars =
        self.used_characters.get(stat_key)
                  627                 if chars is not None and
        len(chars[1]):
/home/alex/Python/lib/python3.4/site-packages/matplotlib/cbook.py in
             __call__(self, path)
                 1020                 stat_key = realpath
                 1021             else:
             -> 1022                 stat = os.stat(realpath)
                 1023                 stat_key = (stat.st_ino,
stat.st_dev)
                 1024             result = realpath, stat_key
FileNotFoundError: [Errno 2] No such file or directory:
             '/home/alex/yt/doc/source/quickstart/cmsy10'

On 25 July 2015 at 05:48, John ZuHone
        mailto:jzuhone@space.mit.edu
             mailto:jzuhone@space.mit.edu>> wrote:
We are proud to announce the release of yt 3.2!
yt (http://yt-project.org) is an open source,
                 community-developed toolkit
                 for analysis and visualization of volumetric data of
        all types,
                 with a
                 particular emphasis on astrophysical simulations and
        nuclear
                 engineering
                 simulations.
Major enhancements
Particle-Only Plots - a series of new plotting
        functions for
                 visualizing
                 particle data.  See here for more information.
                 Late-stage beta support for Python 3 - unit tests and
        answer
                 tests pass for
                 all the major frontends under python 3.4, and yt should
        now be
                 mostly if not
                 fully usable.  Because many of the yt developers are
        still on
                 Python 2 at
                 this point, this should be considered a “late stage
        beta” as
                 there may be
                 remaining issues yet to be identified or worked out.
                 Now supporting Gadget Friend-of-Friends/Subfind
        catalogs - see
                 here to learn
                 how to load halo catalogs as regular yt datasets.
                 Custom colormaps can now be easily defined and added -
        see here
                 to learn
                 how!
                 Now supporting Fargo3D data
                 Performance improvements throughout the code base for
        memory and
                 speed
Minor enhancements
Various updates to the following frontends: ART,
        Athena, Castro,
                 Chombo,
                 Gadget, GDF, Maestro, Pluto, RAMSES, Rockstar, SDF,
Tipsy
                 Numerous documentation updates
                 Generic hexahedral mesh pixelizer
                 Adding annotate_ray() callback for plots
                 AbsorptionSpectrum returned to full functionality and
        now using
                 faster SciPy
                 Voigt profile
                 Add a color_field argument to annotate_streamline
                 Smoothing lengths auto-calculated for Tipsy Datasets
                 Adding SimulationTimeSeries support for Gadget and
OWLS.
                 Generalizing derived quantity outputs to all be
        YTArrays or lists of
                 YTArrays as appropriate
                 Star analysis returned to full functionality
                 FITS image writing refactor
                 Adding gradient fields on the fly
                 Adding support for Gadget Nx4 metallicity fields
                 Updating value of solar metal mass fraction to be
        consistent
                 with Cloudy.
                 Gadget raw binary snapshot handling & non-cosmological
                 simulation units
                 Adding support for LightRay class to work with
Gadget+Tipsy
                 Add support for subclasses of frontends
                 Dependencies updated
                 Serialization for projections using minimal
representation
                 Adding Grid visitors in Cython
                 Improved semantics for derived field units
                 Add a yaw() method for the PerspectiveCamera + switch
        back to LHS
                 Adding annotate_clear() function to remove previous
        callbacks
                 from a plot
                 Added documentation for hexahedral mesh on website
                 Speed up nearest neighbor evaluation
                 Add a convenience method to create deposited particle
        fields
                 UI and docs updates for 3D streamlines
                 Ensure particle fields are tested in the field unit
tests
                 Allow a suffix to be specified to save()
                 Add profiling using airspeed velocity
                 Various plotting enhancements and bugfixes
                 Use hglib to update
                 Various minor updates to halo_analysis toolkit
                 Docker-based tests for install_script.sh
                 Adding support for single and non-cosmological datasets
        to LightRay
                 Adding the Pascal unit
                 Add weight_field to PPVCube
                 FITS reader: allow HDU in auxiliary
                 Fixing electromagnetic units
                 Specific Angular Momentum [xyz] computed relative to a
        normal vector
Bugfixes
Adding ability to create union fields from alias fields
                 Small fix to allow enzo AP datasets to load in parallel
        when no
                 APs present
                 Use proper cell dimension in gradient function.
                 Minor memory optimization for smoothed particle fields
                 Fix thermal_energy for Enzo HydroMethod==6
                 Make sure annotate_particles handles unitful widths
        properly
                 Improvements for add_particle_filter and
particle_filter
                 Specify registry in off_axis_projection's image
        finalization
                 Apply fix for particle momentum units to the boxlib
        frontend
                 Avoid traceback in "yt version" when python-hglib is
        not installed
                 Expose no_ghost from export_sketchfab down to
                 _extract_isocontours_from_grid
                 Fix broken magnetic_unit attribute
                 Fixing an off-by-one error in the set x/y lim methods
for
                 profile plots
                 Providing better error messages to PlotWindow callbacks
                 Updating annotate_timestamp to avoid auto-override
                 Updating callbacks to consistently define coordinate
system
                 Fixing species fields for OWLS and tipsy
                 Fix extrapolation for vertex-centered data
                 Fix periodicity check in FRBs
                 Rewrote project_to_plane() in PerspectiveCamera for
        draw_domain()
                 Fix intermittent failure in
        test_add_deposited_particle_field
                 Improve minorticks for a symlog plot with one-sided
data
                 Fix smoothed covering grid cell computation
                 Absorption spectrum generator now 3.0 compliant
                 Fix off-by-one-or-more in particle smallest dx
                 Fix dimensionality mismatch error in covering grid
                 Fix curvature term in cosmology calculator
                 Fix geographic axes and pixelization
                 Ensure axes aspect ratios respect the user-selected
        plot aspect
                 ratio
                 Avoid clobbering field_map when calling
profile.add_fields
                 Fixing the arbitrary grid deposit code
                 Fix spherical plotting centering
                 Make the behavior of to_frb consistent with the
docstring
                 Ensure projected units are initialized when there are
        no chunks.
                 Removing "field already exists" warnings from the
Owls and
                 Gadget frontends
                 Various photon simulator bugs
                 Fixed use of LaTeX math mode
                 Fix upload_image
                 Enforce plot width in CSS when displayed in a notebook
                 Fix cStringIO.StringIO -> cStringIO in png_writer
                 Add some input sanitizing and error checking to
        covering_grid
                 initializer
                 Fix for geographic plotting
                 Use the correct filename template for single-file OWLS
        datasets.
                 Fix Enzo IO performance for 32 bit datasets
                 Adding a number density field for Enzo MultiSpecies=0
        datasets.
                 Fix RAMSES block ordering
                 Fix ART star particle masses to correctly reflect
        current and
                 initial mass
                 Updating ragged array tests for NumPy 1.9.1
                 Force returning lists for HDF5FileHandler
Coming Soon!
The next major release of yt will be version 3.3,
which is
                 slated to include
                 an overhaul of the volume rendering system and
support for
                 analyzing and
                 visualizing unstructured mesh data.
Standard Installation Methods
As with previous releases, you can install yt from
        source using
                 one of the
                 following methods.
1) From the install script
(http://yt-project.org/#getyt ):
Note, many of the dependencies have been updated since
        version
                 3.1.  If you
                 previously installed yt from the install script, it is
        advised
                 that you
                 re-install yt from scratch.
# Installation
$ wget
http://bitbucket.org/yt_analysis/yt/raw/stable/doc/install_script.sh
                 $ bash install_script.sh
# Update
$ yt update
2) From pip (source or binary wheel, see below for more
        details):
# Installation
$ pip install yt
# Update
$ pip install -U yt
3) From the Anaconda Python Distribution
                 (https://store.continuum.io/cshop/anaconda/):
# Installation
$ conda install yt
# Update
$ conda update yt
Note that it might take a day or two for the conda
        package to be
                 updated.
If you are on the “stable” branch, updating will bring
        you from
                 yt 3.1 to
                 3.2, incorporating all
                 changes since 3.1, whereas if you are on the “dev” or
“yt”
                 branch, only the
                 changes since
                 your last update should be incorporated.
Installing Binary Packages via pip
New to this release is the ability to install binary
        packages
                 (“wheels”)
                 using pip on Windows and Mac OS X (64-bit only for
        both). This
                 has the
                 advantage of not needing to install yt from source
using a
                 proper compiler
                 setup, which has caused occasional problems on both of
        these
                 platforms and
                 prevented us from installing yt easily on other Python
                 distributions.
We have so far been able to install and run the binary
                 distribution via pip
                 on the following platforms and Python stacks:
Note that it might take a day or two for the pip wheels
        to be
                 updated.
Windows x86_64:
Enthought Canopy Python
        (https://www.enthought.com/products/canopy/)
                 WinPython (http://winpython.sourceforge.net/)
Mac OS X x86_64:
Enthought Canopy Python
        (https://www.enthought.com/products/canopy/)
                 Homebrew Python (http://brew.sh/)
                 Python.org Python
                 Mac OS X’s system Python
                 MacPorts Python (https://www.macports.org/)
This is somewhat experimental, so other distributions
        may work
                 (or not),
                 please submit bug reports or successes to the mailing
        list or to the
                 Bitbucket issues page
        (http://bitbucket.org/yt_analysis/yt/issues).
All distributions are recommended to be Python v. 2.7,
        although
                 with yt 3.2
                 there is late-stage beta support for Python 3.4. The
                 requirements for
                 installing yt via this method are the same as from
source:
NumPy
                 h5py
                 HDF5
                 SymPy
                 Matplotlib
                 IPython (not required, but strongly recommended)
To install a new version of yt on one of these
        platforms, simply do
$ pip install yt
and you should get the binary distribution
        automatically. Also,
                 if your
                 python installation is system-wide (e.g., the Mac
        system Python)
                 you might
                 need to run pip with administrator privileges.
For more information, including more installation
        instructions,
                 links to
                 community resources, and information on contributing to
        yt’s
                 development,
                 please see the yt homepage at http://yt-project.org
and the
                 documentation
                 for yt-3.2 at http://yt-project.org/docs/3.2.
yt is the product of a large community of developers
        and users
                 and we are
                 extraordinarily grateful for and proud of their
        contributions.
                 Please
                 forward this announcement on to any interested parties.
As always, if you have any questions, concerns, or run
        into any
                 trouble
                 updating please don't hesitate to send a message to the
        mailing
                 list or stop
                 by our IRC channel.
All the best,
                 The yt development team
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