Hi Patrick, Is this a cosmology simulation? If so, I think the issue is that the window is in physical coordinates, which are increasing with time. Britton On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum wrote:

Hi Patrick,

I'm unable to reproduce the issue you're seeing. I'm running the following script:

from yt.mods import * # set up our namespace from yt.analysis_modules.level_**sets.api import *

pf = load("galaxy0030/galaxy0030")

master_clump = pf.h.load_object('My_Clumps')

all_clumps = get_lowest_clumps(master_**clump)

for i in range(1,3):

prj = ProjectionPlot(pf,2,'Density',**center='c')

prj.set_width((20,'kpc'))

slc.annotate_text([0.0,1.05], "Clump %s" % i)

slc.annotate_clumps([all_**clumps[i]])

slc.save(str(i))

I've previously saved the clump objects in the file "My_clumps". I did this following Britton's recipe from the workshop:

https://bitbucket.org/**brittonsmith/yt.workshop2012.**clump-finding/src/* *1e7af99cec95fb307bb79055f908d3**9a200b7091/scripts/find_** clumps_and_save.py?at=defaulthttps://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99...

When I run the script, I get the following two images:

http://i.imgur.com/MhkaQ.png http://i.imgur.com/ZGzTl.png

This script uses the IsolatedGalaxy dataset stored at yt-project.org/data

It would help me track down what's going wrong if you could come up with a somewhat simpler script that reproduces the error, preferably using one of the datasets on yt-project.org. Please feel free to e-mail me in private or join us on irc so we can iterate on this.

Cheers,

Nathan

On 11/12/12 9:50 AM, Patrick Rieser wrote:

...

Hey all,

So I still get some strange behaviour with the ProjectionPlot. If I use the projection.set_width() with the clumps callback method I get the real image shrinked inside the the plot window. Strange thing is, that it grows with each step! Here is a demonstration how it looks (you have to look closely as it doesn't grow that much each step):

http://www.flickr.com/photos/**87912862@N05/sets/**72157631990474435/http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/

If I don't use the set_width() then the image itself looks fine, but the scale on the axis grows with each step. So it seems to be the same error than with fixed width.

Best wishes, Patrick

Here is the code that I am using:

# ID is just a list of tuples with clumps/their position in an array # sim_files and clump_files is a list containing the filenames # get_myclump() simply returns a specific clump

for j, series in enumerate(ID): for i in series: pf = load(sim_files[i[0]]) myclump = get_myclump(clump_files[i[0]], i[1])

pc = ProjectionPlot(pf, axis, my_field, center = pf.domain_center, weight_field = my_wfield) pc.set_width(28, "mpc") pc.annotate_text([0.0,1.05], "Clump %s" % j)

if redshift: pc.annotate_text([0.917,1.05], "z = %0.4f" % pf.current_redshift) if grid: pc.annotate_grids() if fix_scale: pc.set_zlim(my_field,**boundaries[0],boundaries[1])

pc.set_cmap("Density", "idl01") pc.annotate_clumps(myclump)

pc.save('%s/Clump_%s_File_%s_**Nr_%s_%s_Projection.png' % (myBASEDIR, j, i[0], i[1], axis)) ______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Ah damn, now I feel stupid. I should have realized that. I will try it tomorrow, but yes, that should fix it! Thanks a lot! Best wishes, Patrick Am 12.11.2012 19:38, schrieb Nathan Goldbaum:

If Britton is correct (and looking closely at your script, I suspect he is) you'll likely fix the issue by specifying the width of the image in comoving units:

pc.set_width((28,'mpccm'))

Right now the plot axes will still choose to annotate the x and y axes using physical units, even though the width of the image will be the comoving width you requested. Sorry for that bit of nonintuitiveness. Sam Skillman just filed a bug about this issue which I will fix soon: https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults

-Nathan

On 11/12/12 10:25 AM, Britton Smith wrote:

...

Hi Patrick,

Is this a cosmology simulation? If so, I think the issue is that the window is in physical coordinates, which are increasing with time.

Britton

On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Patrick,

I'm unable to reproduce the issue you're seeing. I'm running the following script:

from yt.mods import * # set up our namespace from yt.analysis_modules.level_sets.api import *

pf = load("galaxy0030/galaxy0030")

master_clump = pf.h.load_object('My_Clumps')

all_clumps = get_lowest_clumps(master_clump)

for i in range(1,3):

prj = ProjectionPlot(pf,2,'Density',center='c')

prj.set_width((20,'kpc'))

slc.annotate_text([0.0,1.05], "Clump %s" % i)

slc.annotate_clumps([all_clumps[i]])

slc.save(str(i))

I've previously saved the clump objects in the file "My_clumps". I did this following Britton's recipe from the workshop:

https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99...

When I run the script, I get the following two images:

http://i.imgur.com/MhkaQ.png http://i.imgur.com/ZGzTl.png

This script uses the IsolatedGalaxy dataset stored at yt-project.org/data http://yt-project.org/data

It would help me track down what's going wrong if you could come up with a somewhat simpler script that reproduces the error, preferably using one of the datasets on yt-project.org http://yt-project.org. Please feel free to e-mail me in private or join us on irc so we can iterate on this.

Cheers,

Nathan

On 11/12/12 9:50 AM, Patrick Rieser wrote:

Hey all,

So I still get some strange behaviour with the ProjectionPlot. If I use the projection.set_width() with the clumps callback method I get the real image shrinked inside the the plot window. Strange thing is, that it grows with each step! Here is a demonstration how it looks (you have to look closely as it doesn't grow that much each step):

http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/

If I don't use the set_width() then the image itself looks fine, but the scale on the axis grows with each step. So it seems to be the same error than with fixed width.

Best wishes, Patrick

Here is the code that I am using:

# ID is just a list of tuples with clumps/their position in an array # sim_files and clump_files is a list containing the filenames # get_myclump() simply returns a specific clump

for j, series in enumerate(ID): for i in series: pf = load(sim_files[i[0]]) myclump = get_myclump(clump_files[i[0]], i[1])

pc = ProjectionPlot(pf, axis, my_field, center = pf.domain_center, weight_field = my_wfield) pc.set_width(28, "mpc") pc.annotate_text([0.0,1.05], "Clump %s" % j)

if redshift: pc.annotate_text([0.917,1.05], "z = %0.4f" % pf.current_redshift) if grid: pc.annotate_grids() if fix_scale: pc.set_zlim(my_field,boundaries[0],boundaries[1])

pc.set_cmap("Density", "idl01") pc.annotate_clumps(myclump)

pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' % (myBASEDIR, j, i[0], i[1], axis)) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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When I try pc.set_width((28,'mpccm')) it raises a key error: Traceback (most recent call last): File "projections.py", line 89, in <module> pc.set_width((28,'mpccm')) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 81, in newfunc rv = f(*args, **kwargs) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 458, in set_width width = [w / self.pf[unit] for w in width] File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 143, in __getitem__ raise KeyError(key) KeyError: 'mpccm' Also when I search through the yt source code, "mpccm" is only found in universal_fields.py (in the WeakLensingConvergence field) and in light_ray.py. Best wishes, Patrick Am 12.11.2012 20:32, schrieb Britton Smith:

Patrick,

Don't worry about it. I do that stuff all the time.

Britton

On Mon, Nov 12, 2012 at 2:26 PM, Patrick Rieser mailto:patrick.rieser@uibk.ac.at> wrote:

Ah damn, now I feel stupid. I should have realized that. I will try it tomorrow, but yes, that should fix it!

Thanks a lot!

Best wishes, Patrick

Am 12.11.2012 19:38, schrieb Nathan Goldbaum:

If Britton is correct (and looking closely at your script, I suspect he is) you'll likely fix the issue by specifying the width of the image in comoving units:

pc.set_width((28,'mpccm'))

Right now the plot axes will still choose to annotate the x and y axes using physical units, even though the width of the image will be the comoving width you requested. Sorry for that bit of nonintuitiveness. Sam Skillman just filed a bug about this issue which I will fix soon: https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults

-Nathan

On 11/12/12 10:25 AM, Britton Smith wrote:

Hi Patrick,

Is this a cosmology simulation? If so, I think the issue is that the window is in physical coordinates, which are increasing with time.

Britton

On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum mailto:nathan12343@gmail.com mailto:nathan12343@gmail.com>> wrote:

Hi Patrick,

I'm unable to reproduce the issue you're seeing. I'm running the following script:

from yt.mods import * # set up our namespace from yt.analysis_modules.level_sets.api import *

pf = load("galaxy0030/galaxy0030")

master_clump = pf.h.load_object('My_Clumps')

all_clumps = get_lowest_clumps(master_clump)

for i in range(1,3):

prj = ProjectionPlot(pf,2,'Density',center='c')

prj.set_width((20,'kpc'))

slc.annotate_text([0.0,1.05], "Clump %s" % i)

slc.annotate_clumps([all_clumps[i]])

slc.save(str(i))

I've previously saved the clump objects in the file "My_clumps". I did this following Britton's recipe from the workshop:

https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99...

When I run the script, I get the following two images:

http://i.imgur.com/MhkaQ.png http://i.imgur.com/ZGzTl.png

This script uses the IsolatedGalaxy dataset stored at yt-project.org/data http://yt-project.org/data http://yt-project.org/data

It would help me track down what's going wrong if you could come up with a somewhat simpler script that reproduces the error, preferably using one of the datasets on yt-project.org http://yt-project.org http://yt-project.org. Please feel free to e-mail me in private or join us on irc so we can iterate on this.

Cheers,

Nathan

On 11/12/12 9:50 AM, Patrick Rieser wrote:

Hey all,

So I still get some strange behaviour with the ProjectionPlot. If I use the projection.set_width() with the clumps callback method I get the real image shrinked inside the the plot window. Strange thing is, that it grows with each step! Here is a demonstration how it looks (you have to look closely as it doesn't grow that much each step):

http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/

If I don't use the set_width() then the image itself looks fine, but the scale on the axis grows with each step. So it seems to be the same error than with fixed width.

Best wishes, Patrick

Here is the code that I am using:

# ID is just a list of tuples with clumps/their position in an array # sim_files and clump_files is a list containing the filenames # get_myclump() simply returns a specific clump

for j, series in enumerate(ID): for i in series: pf = load(sim_files[i[0]]) myclump = get_myclump(clump_files[i[0]], i[1])

pc = ProjectionPlot(pf, axis, my_field, center = pf.domain_center, weight_field = my_wfield) pc.set_width(28, "mpc") pc.annotate_text([0.0,1.05], "Clump %s" % j)

if redshift: pc.annotate_text([0.917,1.05], "z = %0.4f" % pf.current_redshift) if grid: pc.annotate_grids() if fix_scale: pc.set_zlim(my_field,boundaries[0],boundaries[1])

pc.set_cmap("Density", "idl01") pc.annotate_clumps(myclump)

pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' % (myBASEDIR, j, i[0], i[1], axis)) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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mpccm doesn't seem to be in the output. Do I have to set a switch somewhere so that it is created? level # grids # cells # cells^3 ---------------------------------------------- 0 1 4096 15 1 8 32768 31 2 64 262144 63 3 512 2097152 127 4 512 2097152 127 5 512 2097152 127 6 512 2097152 127 7 512 2097152 127 ---------------------------------------------- 2633 10784768 t = 3.03585620e+17 = 3.03585620e+17 s = 9.62004779e+09 years Smallest Cell: Width: 4.883e-04 unitary Width: 1.562e-02 mpc Width: 1.562e+01 kpc Width: 1.562e+04 pc Width: 3.223e+09 au Width: 6.934e+11 rsun Width: 2.995e+17 miles Width: 4.821e+22 cm Width: 4.821e+22 1 Best wishes, Patrick Am 13.11.2012 14:55, schrieb Matthew Turk:

Hi Patrick,

It gets autocreated by concatenating "mpc" with "cm", so it won't show up directly in the source. If you run pf.h.print_stats() it will print out all the available length units -- what shows up in there?

-Matt

On Tue, Nov 13, 2012 at 7:55 AM, Patrick Rieser wrote:

...

When I try

pc.set_width((28,'mpccm'))

it raises a key error:

Traceback (most recent call last): File "projections.py", line 89, in <module> pc.set_width((28,'mpccm')) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 81, in newfunc rv = f(*args, **kwargs) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 458, in set_width width = [w / self.pf[unit] for w in width] File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 143, in __getitem__ raise KeyError(key) KeyError: 'mpccm'

Also when I search through the yt source code, "mpccm" is only found in universal_fields.py (in the WeakLensingConvergence field) and in light_ray.py.

Best wishes, Patrick

Am 12.11.2012 20:32, schrieb Britton Smith:

Patrick,

Don't worry about it. I do that stuff all the time.

Britton

On Mon, Nov 12, 2012 at 2:26 PM, Patrick Rieser wrote:

...

Ah damn, now I feel stupid. I should have realized that. I will try it tomorrow, but yes, that should fix it!

Thanks a lot!

Best wishes, Patrick

Am 12.11.2012 19:38, schrieb Nathan Goldbaum:

...

If Britton is correct (and looking closely at your script, I suspect he is) you'll likely fix the issue by specifying the width of the image in comoving units:

pc.set_width((28,'mpccm'))

Right now the plot axes will still choose to annotate the x and y axes using physical units, even though the width of the image will be the comoving width you requested. Sorry for that bit of nonintuitiveness. Sam Skillman just filed a bug about this issue which I will fix soon: https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults

-Nathan

On 11/12/12 10:25 AM, Britton Smith wrote:

...

Hi Patrick,

Is this a cosmology simulation? If so, I think the issue is that the window is in physical coordinates, which are increasing with time.

Britton

On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum mailto:nathan12343@gmail.com> wrote:

Hi Patrick,

I'm unable to reproduce the issue you're seeing. I'm running the following script:

from yt.mods import * # set up our namespace from yt.analysis_modules.level_sets.api import *

pf = load("galaxy0030/galaxy0030")

master_clump = pf.h.load_object('My_Clumps')

all_clumps = get_lowest_clumps(master_clump)

for i in range(1,3):

prj = ProjectionPlot(pf,2,'Density',center='c')

prj.set_width((20,'kpc'))

slc.annotate_text([0.0,1.05], "Clump %s" % i)

slc.annotate_clumps([all_clumps[i]])

slc.save(str(i))

I've previously saved the clump objects in the file "My_clumps". I did this following Britton's recipe from the workshop:

https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99...

When I run the script, I get the following two images:

http://i.imgur.com/MhkaQ.png http://i.imgur.com/ZGzTl.png

This script uses the IsolatedGalaxy dataset stored at yt-project.org/data http://yt-project.org/data

It would help me track down what's going wrong if you could come up with a somewhat simpler script that reproduces the error, preferably using one of the datasets on yt-project.org http://yt-project.org. Please feel free to e-mail me in private or join us on irc so we can iterate on this.

Cheers,

Nathan

On 11/12/12 9:50 AM, Patrick Rieser wrote:

Hey all,

So I still get some strange behaviour with the ProjectionPlot. If I use the projection.set_width() with the clumps callback method I get the real image shrinked inside the the plot window. Strange thing is, that it grows with each step! Here is a demonstration how it looks (you have to look closely as it doesn't grow that much each step):

http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/

If I don't use the set_width() then the image itself looks fine, but the scale on the axis grows with each step. So it seems to be the same error than with fixed width.

Best wishes, Patrick

Here is the code that I am using:

# ID is just a list of tuples with clumps/their position in an array # sim_files and clump_files is a list containing the filenames # get_myclump() simply returns a specific clump

for j, series in enumerate(ID): for i in series: pf = load(sim_files[i[0]]) myclump = get_myclump(clump_files[i[0]], i[1])

pc = ProjectionPlot(pf, axis, my_field, center = pf.domain_center, weight_field = my_wfield) pc.set_width(28, "mpc") pc.annotate_text([0.0,1.05], "Clump %s" % j)

if redshift: pc.annotate_text([0.917,1.05], "z = %0.4f" % pf.current_redshift) if grid: pc.annotate_grids() if fix_scale: pc.set_zlim(my_field,boundaries[0],boundaries[1])

pc.set_cmap("Density", "idl01") pc.annotate_clumps(myclump)

pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' % (myBASEDIR, j, i[0], i[1], axis)) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org mailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Yes, it's a flash dataset. Thanks a lot! Best wishes, Patrick Am 13.11.2012 15:07, schrieb Matthew Turk:

Hi Patrick,

Is this a FLASH dataset, by any chance? If so, I think I know the problem for why it is not adding the units. I will take a look and get back to you.

Matt

On Nov 13, 2012 9:00 AM, "Patrick Rieser" mailto:patrick.rieser@uibk.ac.at> wrote:

mpccm doesn't seem to be in the output. Do I have to set a switch somewhere so that it is created?

level # grids # cells # cells^3 ---------------------------------------------- 0 1 4096 15 1 8 32768 31 2 64 262144 63 3 512 2097152 127 4 512 2097152 127 5 512 2097152 127 6 512 2097152 127 7 512 2097152 127 ---------------------------------------------- 2633 10784768

t = 3.03585620e+17 = 3.03585620e+17 s = 9.62004779e+09 years

Smallest Cell: Width: 4.883e-04 unitary Width: 1.562e-02 mpc Width: 1.562e+01 kpc Width: 1.562e+04 pc Width: 3.223e+09 au Width: 6.934e+11 rsun Width: 2.995e+17 miles Width: 4.821e+22 cm Width: 4.821e+22 1

Best wishes, Patrick

Am 13.11.2012 14:55, schrieb Matthew Turk:

Hi Patrick,

It gets autocreated by concatenating "mpc" with "cm", so it won't show up directly in the source. If you run pf.h.print_stats() it will print out all the available length units -- what shows up in there?

-Matt

On Tue, Nov 13, 2012 at 7:55 AM, Patrick Rieser mailto:patrick.rieser@uibk.ac.at> wrote:

When I try

pc.set_width((28,'mpccm'))

it raises a key error:

Traceback (most recent call last): File "projections.py", line 89, in <module> pc.set_width((28,'mpccm')) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 81, in newfunc rv = f(*args, **kwargs) File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 458, in set_width width = [w / self.pf http://self.pf[unit] for w in width] File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 143, in __getitem__ raise KeyError(key) KeyError: 'mpccm'

Also when I search through the yt source code, "mpccm" is only found in universal_fields.py (in the WeakLensingConvergence field) and in light_ray.py.

Best wishes, Patrick

Am 12.11.2012 20:32, schrieb Britton Smith:

Patrick,

Don't worry about it. I do that stuff all the time.

Britton

On Mon, Nov 12, 2012 at 2:26 PM, Patrick Rieser mailto:patrick.rieser@uibk.ac.at> wrote:

Ah damn, now I feel stupid. I should have realized that. I will try it tomorrow, but yes, that should fix it!

Thanks a lot!

Best wishes, Patrick

Am 12.11.2012 19:38, schrieb Nathan Goldbaum:

If Britton is correct (and looking closely at your script, I suspect he is) you'll likely fix the issue by specifying the width of the image in comoving units:

pc.set_width((28,'mpccm'))

Right now the plot axes will still choose to annotate the x and y axes using physical units, even though the width of the image will be the comoving width you requested. Sorry for that bit of nonintuitiveness. Sam Skillman just filed a bug about this issue which I will fix soon: https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults

-Nathan

On 11/12/12 10:25 AM, Britton Smith wrote:

Hi Patrick,

Is this a cosmology simulation? If so, I think the issue is that the window is in physical coordinates, which are increasing with time.

Britton

On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum mailto:nathan12343@gmail.com mailto:nathan12343@gmail.com>> wrote:

Hi Patrick,

I'm unable to reproduce the issue you're seeing. I'm running the following script:

from yt.mods import * # set up our namespace from yt.analysis_modules.level_sets.api import *

pf = load("galaxy0030/galaxy0030")

master_clump = pf.h.load_object('My_Clumps')

all_clumps = get_lowest_clumps(master_clump)

for i in range(1,3):

prj = ProjectionPlot(pf,2,'Density',center='c')

prj.set_width((20,'kpc'))

slc.annotate_text([0.0,1.05], "Clump %s" % i)

slc.annotate_clumps([all_clumps[i]])

slc.save(str(i))

I've previously saved the clump objects in the file "My_clumps". I did this following Britton's recipe from the workshop:

https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99...

When I run the script, I get the following two images:

http://i.imgur.com/MhkaQ.png http://i.imgur.com/ZGzTl.png

This script uses the IsolatedGalaxy dataset stored at yt-project.org/data http://yt-project.org/data http://yt-project.org/data

It would help me track down what's going wrong if you could come up with a somewhat simpler script that reproduces the error, preferably using one of the datasets on yt-project.org http://yt-project.org http://yt-project.org. Please feel free to e-mail me in private or join us on irc so we can iterate on this.

Cheers,

Nathan

On 11/12/12 9:50 AM, Patrick Rieser wrote:

Hey all,

So I still get some strange behaviour with the ProjectionPlot. If I use the projection.set_width() with the clumps callback method I get the real image shrinked inside the the plot window. Strange thing is, that it grows with each step! Here is a demonstration how it looks (you have to look closely as it doesn't grow that much each step):

http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/

If I don't use the set_width() then the image itself looks fine, but the scale on the axis grows with each step. So it seems to be the same error than with fixed width.

Best wishes, Patrick

Here is the code that I am using:

# ID is just a list of tuples with clumps/their position in an array # sim_files and clump_files is a list containing the filenames # get_myclump() simply returns a specific clump

for j, series in enumerate(ID): for i in series: pf = load(sim_files[i[0]]) myclump = get_myclump(clump_files[i[0]], i[1])

pc = ProjectionPlot(pf, axis, my_field, center = pf.domain_center, weight_field = my_wfield) pc.set_width(28, "mpc") pc.annotate_text([0.0,1.05], "Clump %s" % j)

if redshift:

pc.annotate_text([0.917,1.05], "z = %0.4f" % pf.current_redshift) if grid: pc.annotate_grids() if fix_scale: pc.set_zlim(my_field,boundaries[0],boundaries[1])

pc.set_cmap("Density", "idl01") pc.annotate_clumps(myclump)

pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' % (myBASEDIR, j, i[0], i[1], axis))

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Thanks for fixing it so fast, you people are really incredible! Best wishes, Patrick Am 13.11.2012 15:15, schrieb Matthew Turk:

Hi Patrick,

I've pushed a fix in 3b328da941be:

https://bitbucket.org/yt_analysis/yt/changeset/3b328da941be8637737b0405e57d6...

If you run "yt update" you should get it. Thanks for catching this!

-Matt

On Tue, Nov 13, 2012 at 9:11 AM, Patrick Rieser wrote:

...

Yes, it's a flash dataset.

Thanks a lot!

Best wishes, Patrick

Am 13.11.2012 15:07, schrieb Matthew Turk:

Hi Patrick,

Is this a FLASH dataset, by any chance? If so, I think I know the problem for why it is not adding the units. I will take a look and get back to you.

Matt

On Nov 13, 2012 9:00 AM, "Patrick Rieser" wrote:

...

mpccm doesn't seem to be in the output. Do I have to set a switch somewhere so that it is created?

level # grids # cells # cells^3 ---------------------------------------------- 0 1 4096 15 1 8 32768 31 2 64 262144 63 3 512 2097152 127 4 512 2097152 127 5 512 2097152 127 6 512 2097152 127 7 512 2097152 127 ---------------------------------------------- 2633 10784768

t = 3.03585620e+17 = 3.03585620e+17 s = 9.62004779e+09 years

Smallest Cell: Width: 4.883e-04 unitary Width: 1.562e-02 mpc Width: 1.562e+01 kpc Width: 1.562e+04 pc Width: 3.223e+09 au Width: 6.934e+11 rsun Width: 2.995e+17 miles Width: 4.821e+22 cm Width: 4.821e+22 1

Best wishes, Patrick

Am 13.11.2012 14:55, schrieb Matthew Turk:

...

Hi Patrick,

It gets autocreated by concatenating "mpc" with "cm", so it won't show up directly in the source. If you run pf.h.print_stats() it will print out all the available length units -- what shows up in there?

-Matt

On Tue, Nov 13, 2012 at 7:55 AM, Patrick Rieser wrote:

...

When I try

pc.set_width((28,'mpccm'))

it raises a key error:

Traceback (most recent call last): File "projections.py", line 89, in <module> pc.set_width((28,'mpccm')) File

"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 81, in newfunc rv = f(*args, **kwargs) File

"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 458, in set_width width = [w / self.pf[unit] for w in width] File

"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 143, in __getitem__ raise KeyError(key) KeyError: 'mpccm'

Also when I search through the yt source code, "mpccm" is only found in universal_fields.py (in the WeakLensingConvergence field) and in light_ray.py.

Best wishes, Patrick

Am 12.11.2012 20:32, schrieb Britton Smith:

Patrick,

Don't worry about it. I do that stuff all the time.

Britton

On Mon, Nov 12, 2012 at 2:26 PM, Patrick Rieser wrote:

...

Ah damn, now I feel stupid. I should have realized that. I will try it tomorrow, but yes, that should fix it!

Thanks a lot!

Best wishes, Patrick

Am 12.11.2012 19:38, schrieb Nathan Goldbaum:

> If Britton is correct (and looking closely at your script, I suspect > he > is) you'll likely fix the issue by specifying the width of the image > in > comoving units: > > pc.set_width((28,'mpccm')) > > Right now the plot axes will still choose to annotate the x and y axes > using physical units, even though the width of the image will be the > comoving width you requested. Sorry for that bit of nonintuitiveness. > Sam > Skillman just filed a bug about this issue which I will fix soon: > > https://bitbucket.org/yt_analysis/yt/issue/463/plotwindow-axes-unit-defaults > > -Nathan > > On 11/12/12 10:25 AM, Britton Smith wrote: >> Hi Patrick, >> >> Is this a cosmology simulation? If so, I think the issue is that the >> window is in physical coordinates, which are increasing with time. >> >> Britton >> >> >> On Mon, Nov 12, 2012 at 1:21 PM, Nathan Goldbaum >> > mailto:nathan12343@gmail.com> wrote: >> >> Hi Patrick, >> >> I'm unable to reproduce the issue you're seeing. I'm running >> the >> following script: >> >> from yt.mods import * # set up our namespace >> from yt.analysis_modules.level_sets.api import * >> >> pf = load("galaxy0030/galaxy0030") >> >> master_clump = pf.h.load_object('My_Clumps') >> >> all_clumps = get_lowest_clumps(master_clump) >> >> for i in range(1,3): >> >> prj = ProjectionPlot(pf,2,'Density',center='c') >> >> prj.set_width((20,'kpc')) >> >> slc.annotate_text([0.0,1.05], "Clump %s" % i) >> >> slc.annotate_clumps([all_clumps[i]]) >> >> slc.save(str(i)) >> >> I've previously saved the clump objects in the file "My_clumps". >> I did this following Britton's recipe from the workshop: >> >> >> >> https://bitbucket.org/brittonsmith/yt.workshop2012.clump-finding/src/1e7af99... >> >> When I run the script, I get the following two images: >> >> http://i.imgur.com/MhkaQ.png >> http://i.imgur.com/ZGzTl.png >> >> This script uses the IsolatedGalaxy dataset stored at >> yt-project.org/data http://yt-project.org/data >> >> It would help me track down what's going wrong if you could come >> up with a somewhat simpler script that reproduces the error, >> preferably using one of the datasets on yt-project.org >> http://yt-project.org. Please feel free to e-mail me in >> private >> or join us on irc so we can iterate on this. >> >> Cheers, >> >> Nathan >> >> >> On 11/12/12 9:50 AM, Patrick Rieser wrote: >> >> Hey all, >> >> So I still get some strange behaviour with the >> ProjectionPlot. >> If I use the projection.set_width() with the clumps callback >> method I get the real image shrinked inside the the plot >> window. Strange thing is, that it grows with each step! Here >> is a demonstration how it looks (you have to look closely as >> it doesn't grow that much each step): >> >> http://www.flickr.com/photos/87912862@N05/sets/72157631990474435/ >> >> If I don't use the set_width() then the image itself looks >> fine, but the scale on the axis grows with each step. So it >> seems to be the same error than with fixed width. >> >> >> Best wishes, >> Patrick >> >> >> >> Here is the code that I am using: >> >> # ID is just a list of tuples with clumps/their position in >> an >> array >> # sim_files and clump_files is a list containing the >> filenames >> # get_myclump() simply returns a specific clump >> >> for j, series in enumerate(ID): >> for i in series: >> pf = load(sim_files[i[0]]) >> myclump = get_myclump(clump_files[i[0]], i[1]) >> >> pc = ProjectionPlot(pf, axis, my_field, center = >> pf.domain_center, weight_field = my_wfield) >> pc.set_width(28, "mpc") >> pc.annotate_text([0.0,1.05], "Clump %s" % j) >> >> if redshift: >> pc.annotate_text([0.917,1.05], "z = %0.4f" % >> pf.current_redshift) >> if grid: >> pc.annotate_grids() >> if fix_scale: >> pc.set_zlim(my_field,boundaries[0],boundaries[1]) >> >> pc.set_cmap("Density", "idl01") >> pc.annotate_clumps(myclump) >> >> pc.save('%s/Clump_%s_File_%s_Nr_%s_%s_Projection.png' >> % (myBASEDIR, j, i[0], i[1], axis)) >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> mailto:yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> mailto:yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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