Hello, Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this. Thank you, Nathan Butcher
Hi Nathan, Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to: @derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)]) I don't believe you need any additional changes inside the source code. Let us know if that fixes it! -Matt On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello,
Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
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Hello Matt, Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects? Thank you, Nathan Butcher On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
Hello,
Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote: lines
that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
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On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello,
Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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The colorbar scaling is similar, and the values have changed. It could be a large shift. It is hard for me to tell from the plot. I have attached the updated plot. Nathan On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com>
wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators =
[ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello,
Using an Enzo dataset, I have written a function to find the
derivative
in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Nathan, How are you centering the slice? This looks somewhat like a difference in the centering. Can you try something like: pc = PlotCollection(pf, 'c') pc.add_slice("GravGradient", "x") pc.save() for both the old and new, and see if they look similar? -Matt On Thu, Jun 14, 2012 at 1:41 PM, Nathan Butcher <butchernate@gmail.com> wrote:
The colorbar scaling is similar, and the values have changed. It could be a large shift. It is hard for me to tell from the plot. I have attached the updated plot.
Nathan
On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello,
Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hello, The images are the same as before. I will try to create a simpler test case to check this field and see if it behaves properly. Thank you for all of the help. Nathan On Thu, Jun 14, 2012 at 1:44 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
How are you centering the slice? This looks somewhat like a difference in the centering. Can you try something like:
pc = PlotCollection(pf, 'c') pc.add_slice("GravGradient", "x") pc.save()
for both the old and new, and see if they look similar?
-Matt
On Thu, Jun 14, 2012 at 1:41 PM, Nathan Butcher <butchernate@gmail.com> wrote:
The colorbar scaling is similar, and the values have changed. It could be a large shift. It is hard for me to tell from the plot. I have attached the updated plot.
Nathan
On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the
extra
zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You
need
one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher < butchernate@gmail.com> wrote:
Hello,
Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this.
Thank you, Nathan Butcher
_______________________________________________ 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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Hi Nathan, On Thu, Jun 14, 2012 at 1:55 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello,
The images are the same as before. I will try to create a simpler test case to check this field and see if it behaves properly. Thank you for all of the help.
Okay, I figured out what is going on. Without spatial validation, this sequence: new_field = na.zeros(data['PotentialField'].shape) new_field[1:-1] = data["PotentialField"][sl_right]/ds new_field[1:-1] -= data["PotentialField"][sl_left]/ds is operating on 1D, mostly unsorted arrays. The points next to each other are probably not in x-order, so this doesn't do much. When you do validate spatial, it oeprates on a grid-by-grid basis, and adjacent points are adjacent spatially. So this is okay, and the correct result is the one with the ValidateSpatial call. -Matt
Nathan
On Thu, Jun 14, 2012 at 1:44 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
How are you centering the slice? This looks somewhat like a difference in the centering. Can you try something like:
pc = PlotCollection(pf, 'c') pc.add_slice("GravGradient", "x") pc.save()
for both the old and new, and see if they look similar?
-Matt
On Thu, Jun 14, 2012 at 1:41 PM, Nathan Butcher <butchernate@gmail.com> wrote:
The colorbar scaling is similar, and the values have changed. It could be a large shift. It is hard for me to tell from the plot. I have attached the updated plot.
Nathan
On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <butchernate@gmail.com> wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that the graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Yup, I agree with your assessment -- there's an edge effect. You need one more thing to get the derivative field working; you need to tell yt to give you an extra zone in each direction. You can do that by changing your decorator for the derived field to:
@derived_field(name = "GravGradientX", validators = [ValidateSpatial(1)])
I don't believe you need any additional changes inside the source code. Let us know if that fixes it!
-Matt
On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher <butchernate@gmail.com> wrote: > Hello, > > Using an Enzo dataset, I have written a function to find the > derivative > in > the x-direction of a field. When I try to plot the derivative, I > see > lines > that throughout the plot that I'm guessing are due to the edges of > cells. > The attached plot is a slice of the x-direction derivative of the > PotentialField viewed down the x-axis, but this error appears in > plots > for > density and pressure as well. I am new to using yt, and I am not > sure > what > is causing this. > > Thank you, > Nathan Butcher > > _______________________________________________ > 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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Okay, makes sense. Thank you. Nathan On Thu, Jun 14, 2012 at 1:57 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Nathan,
Hello,
The images are the same as before. I will try to create a simpler test case to check this field and see if it behaves properly. Thank you for all of
On Thu, Jun 14, 2012 at 1:55 PM, Nathan Butcher <butchernate@gmail.com> wrote: the
help.
Okay, I figured out what is going on.
Without spatial validation, this sequence:
new_field = na.zeros(data['PotentialField'].shape) new_field[1:-1] = data["PotentialField"][sl_right]/ds new_field[1:-1] -= data["PotentialField"][sl_left]/ds
is operating on 1D, mostly unsorted arrays. The points next to each other are probably not in x-order, so this doesn't do much. When you do validate spatial, it oeprates on a grid-by-grid basis, and adjacent points are adjacent spatially.
So this is okay, and the correct result is the one with the ValidateSpatial call.
-Matt
Nathan
On Thu, Jun 14, 2012 at 1:44 PM, Matthew Turk <matthewturk@gmail.com>
Hi Nathan,
How are you centering the slice? This looks somewhat like a difference in the centering. Can you try something like:
pc = PlotCollection(pf, 'c') pc.add_slice("GravGradient", "x") pc.save()
for both the old and new, and see if they look similar?
-Matt
On Thu, Jun 14, 2012 at 1:41 PM, Nathan Butcher <butchernate@gmail.com> wrote:
The colorbar scaling is similar, and the values have changed. It could be a large shift. It is hard for me to tell from the plot. I have attached the updated plot.
Nathan
On Thu, Jun 14, 2012 at 1:32 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Thu, Jun 14, 2012 at 1:31 PM, Nathan Butcher <
butchernate@gmail.com>
wrote:
Hello Matt,
Thanks, that seems to have done fixed the issue. I am seeing that
graph looks very different now compared to before. Would forgetting the extra zone change the appearance of the overall plot beyond edge effects?
It should shift the derivative considerably, but the only other differences should be at the edges. Are the actual values different, or is the colorbar scaling differently now?
Thank you, Nathan Butcher
On Thu, Jun 14, 2012 at 1:21 PM, Matthew Turk <
matthewturk@gmail.com>
wrote: > > Hi Nathan, > > Yup, I agree with your assessment -- there's an edge effect. You > need > one more thing to get the derivative field working; you need to tell > yt to give you an extra zone in each direction. You can do that by > changing your decorator for the derived field to: > > @derived_field(name = "GravGradientX", validators = > [ValidateSpatial(1)]) > > I don't believe you need any additional changes inside the source > code. Let us know if that fixes it! > > -Matt > > On Thu, Jun 14, 2012 at 1:14 PM, Nathan Butcher > <butchernate@gmail.com> > wrote: > > Hello, > > > > Using an Enzo dataset, I have written a function to find the > > derivative > > in > > the x-direction of a field. When I try to plot the derivative, I > > see > > lines > > that throughout the plot that I'm guessing are due to the edges of > > cells. > > The attached plot is a slice of the x-direction derivative of
wrote: the the
> > PotentialField viewed down the x-axis, but this error appears in > > plots > > for > > density and pressure as well. I am new to using yt, and I am not > > sure > > what > > is causing this. > > > > Thank you, > > Nathan Butcher > > > > _______________________________________________ > > 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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participants (2)
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Nathan Butcher