AttributeError: cos

[antolikjan]

Context: fresh topographica install on Eddie (from git). Installed pillow,matplotlib and numpy into virtualenv (via pip).

When trying to run my simulation I am getting the error below.

Traceback (most recent call last): File "/exports/work/inf_ndtc/s0570140/NEW_ENVIRONMENT/topographica/topo/command/init.py", line 849, in call topo.sim.run(run_to - topo.sim.time()) File "/exports/work/inf_ndtc/s0570140/NEW_ENVIRONMENT/topographica/topo/base/simulation.py", line 1357, in run event(self) File "/exports/work/inf_ndtc/s0570140/NEW_ENVIRONMENT/topographica/topo/base/simulation.py", line 530, in call self.fn(_self.args,__self.kw) File "/exports/work/inf_ndtc/s0570140/NEW_ENVIRONMENT/topographica/topo/misc/generatorsheet.py", line 103, in generate self.activity[:] = self.input_generator() File "/exports/work/inf_ndtc/s0570140/NEW_ENVIRONMENT/topographica/contrib/CCLISSOM_push_pull_extra.py", line 71, in call return generator(xdensity=xdensity, ydensity=ydensity, bounds=bounds, x=self.x + self.jitter_magnitude * self.r(), y=self.y + self.jitter_magnitude * self.r(), orientation=self.inspect_value("orientation"), index=self.inspect_value("index")) File "/exports/home/s0570140/go_new/topographica/external/imagen/imagen/patterngenerator.py", line 140, in call self._setup_xy(p.bounds,p.xdensity,p.ydensity,p.x,p.y,p.orientation) File "/exports/home/s0570140/go_new/topographica/external/imagen/imagen/patterngenerator.py", line 166, in _setup_xy self.pattern_x, self.pattern_y = self._create_and_rotate_coordinate_arrays(x_points-x,y_points-y,orientation) File "/exports/home/s0570140/go_new/topographica/external/imagen/imagen/patterngenerator.py", line 193, in _create_and_rotate_coordinate_arrays pattern_y = subtract.outer(cos(orientation)_y, sin(orientation)*x) AttributeError: cos

[jbednar]

That's bizarre. In my copy of the code, line 11 of patterngenerator.py does "from numpy import add,subtract,cos,sin", which should clearly provide a definition for cos. Can you check that the same is true for your copy of the file? I can't run your CCLISSOM_push_pull_extra.py example, but everything works fine for tiny.ty at least, at my end.

One clue might be that your virtualenv directory is NEW_ENVIRONMENT/topographica, but it seems to be getting imagen from go_new/topographica; maybe you didn't install the submodules in the virtualenv version and it's finding some old version of imagen? Not sure, really.

[antolikjan]

Hello Jim,

On Tue, Dec 18, 2012 at 5:43 PM, James A. Bednar notifications@github.comwrote:

That's bizarre. In my copy of the code, line 11 of patterngenerator.py does "from numpy import add,subtract,cos,sin", which should clearly provide a definition for cos. Can you check that the same is true for your copy of the file? I can't run your CCLISSOM_push_pull_extra.py example, but everything works fine for tiny.ty at least, at my end.

One clue might be that your virtualenv directory is NEW_ENVIRONMENT/topographica, but it seems to be getting imagen from go_new/topographica; maybe you didn't install the submodules in the virtualenv version and it's finding some old version of imagen? Not sure, really.

That doesn't seem to be a problem bacause the go_new is in fact a symbolic link to the NEW_ENVIRONMENT directory (I even did a diff on the patterngenerator.py file with both version of the path and there is indeed no difference). I don't know why the trace switches between using the 'true' path and the one via the symbolic link, but I cannot imagine that to be a problem.

—

Reply to this email directly or view it on GitHubhttps://github.com/ioam/topographica/issues/496#issuecomment-11494477.

[jbednar]

Ok, so ignoring the strange but harmless go_new behavior, what's the answer to whether your copy of patterngenerator.py does in fact import cos before it's used?

[antolikjan]

line 11: from numpy import add,subtract,cos,sin

This is really bizarre.

On Wed, Dec 19, 2012 at 2:21 PM, James A. Bednar notifications@github.comwrote:

Ok, so ignoring the strange but harmless go_new behavior, what's the answer to whether your copy of patterngenerator.py does in fact import cos before it's used?

— Reply to this email directly or view it on GitHubhttps://github.com/ioam/topographica/issues/496#issuecomment-11529698.

[jbednar]

Inexplicable. It's strange that it's an AttributeError, as well. E.g. I just took my copy of patterngenerator.py, and removed the import of cos, in which case I get "NameError: global name 'cos' is not defined". The only way I can get an AttributeError is by doing x.a, where a is not the name of an attribute of x. Otherwise Python is looking for a global name, and raising a NameError when it doesn't find it.

I don't think I can do any further debugging without a runnable copy of the .ty file that led to the error; maybe one of them is redefining cos or something else crazy like that...

[antolikjan]

Hello Jim,

I am going to investigate this further. In any case, if you clone my topographica contrib repo:

https://github.com/antolikjan/topographica-contrib

you can run the model with this command:

./topographica/topographica -ac "ImageScale=0.45;AFF_lr=0.5;MUE=0.01;MUI=0.01;SETAE=0.004;SETAI=0.002;default_density=20;LGNStr=4.5;SEEStr=0.1;SEIStr=1.0;SIEStr=-2.0;SIIStr=-1.0;Inbalance=0.0;reset_period=40;SS=1;PP_lr=0.1" ./topographica/contrib/CCLISSOM_push_pull.ty -c "topo.sim.run(100)"

(assuming you cloned into the topographica directory)

I should stress that I seem to get this error only on eddie, not on my desktop installation.

Jan

On Wed, Dec 19, 2012 at 2:51 PM, James A. Bednar notifications@github.comwrote:

Inexplicable. It's strange that it's an AttributeError, as well. E.g. I just took my copy of patterngenerator.py, and removed the import of cos, in which case I get "NameError: global name 'cos' is not defined". The only way I can get an AttributeError is by doing x.a, where a is not the name of an attribute of x. Otherwise Python is looking for a global name, and raising a NameError when it doesn't find it.

I don't think I can do any further debugging without a runnable copy of the .ty file that led to the error; maybe one of them is redefining cos or something else crazy like that...

— Reply to this email directly or view it on GitHubhttps://github.com/ioam/topographica/issues/496#issuecomment-11530509.

[jlstevens]

This issue is quite old now - Philipp and I are currently using Topographica on Eddie regularly without any problem. If this is still an issue please reopen it!