Error when plotting negative values on log scale

Community matplotlib-users
1

Hi,

When I do an errorbar plot (a.errorbar(), a = axis) with negative values and then try to change the yscale to log (a.set_yscale(‘log’)) matplotlib crashes with:

Traceback (most recent call last):
File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )
File “/home/specuser/new_workspace/TestDriven/src/RAWPlot.py”, line 371, in plotSASM
line, ec, el = a.errorbar(sasm.q[q_min:q_max], sasm.i[q_min:q_max], sasm.err[q_min:q_max], picker = 3, label = legend_label, **kwargs)
File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 4872, in errorbar
barcols.append( self.vlines(x, lower, upper, **lines_kw) )
File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 3302, in vlines
self.autoscale_view()
File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 1627, in autoscale_view
YL = self.yaxis.get_major_locator().view_limits(y0, y1)
File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1119, in view_limits
if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base)
File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1030, in is_decade
return lx==int(lx)
OverflowError: cannot convert float infinity to integer
Traceback (most recent call last):
File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )
File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 1953, in addItem
newItem = ManipItemPanel(self.underpanel, sasm, font_colour = item_colour)
File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 2353, in init
color = conv.to_rgb(self.sasm.line.get_mfc())
AttributeError: ‘NoneType’ object has no attribute ‘get_mfc’

I don’t think this should be the expected outcome… rather it should not plot values that are illegal/negative (i.e. ignore them).

Is there a way I can get around this without having to search through my data and remove points that are negative or NaN or INF when the yscale needs to be log? That would also show an incorrect curve since a line would be drawn across the points that were removed… It should rather be gaps in the line.

Thanks,
Soren

2

2011/3/10 Søren Nielsen <soren.skou.nielsen@...287...>:

Is there a way I can get around this without having to search through my
data and remove points that are negative or NaN or INF when the yscale needs
to be log? That would also show an incorrect curve since a line would be
drawn across the points that were removed.. It should rather be gaps in the
line.

You can use masked arrays. Masked values don't get plotted. Sample
code (not tested):

import numpy.ma as ma # masked arrays module
...
mdata = ma.masked_array(data)
mdata[mdata <= 0] = ma.masked
plot(mdata)

Goyo

3

2011/3/10 Søren Nielsen <soren.skou.nielsen@…287…>

Hi,

When I do an errorbar plot (a.errorbar(), a = axis) with negative values and then try to change the yscale to log (a.set_yscale(‘log’)) matplotlib crashes with:

Traceback (most recent call last):

File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )

File “/home/specuser/new_workspace/TestDriven/src/RAWPlot.py”, line 371, in plotSASM

line, ec, el = a.errorbar(sasm.q[q_min:q_max], sasm.i[q_min:q_max], sasm.err[q_min:q_max], picker = 3, label = legend_label, **kwargs)

File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 4872, in errorbar

barcols.append( self.vlines(x, lower, upper, **lines_kw) )

File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 3302, in vlines
self.autoscale_view()
File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 1627, in autoscale_view

YL = self.yaxis.get_major_locator().view_limits(y0, y1)

File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1119, in view_limits
if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base)

File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1030, in is_decade
return lx==int(lx)
OverflowError: cannot convert float infinity to integer
Traceback (most recent call last):

File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )

File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 1953, in addItem

newItem = ManipItemPanel(self.underpanel, sasm, font_colour = item_colour)

File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 2353, in init
color = conv.to_rgb(self.sasm.line.get_mfc())

AttributeError: ‘NoneType’ object has no attribute ‘get_mfc’

I don’t think this should be the expected outcome… rather it should not plot values that are illegal/negative (i.e. ignore them).

Is there a way I can get around this without having to search through my data and remove points that are negative or NaN or INF when the yscale needs to be log? That would also show an incorrect curve since a line would be drawn across the points that were removed… It should rather be gaps in the line.

Thanks,
Soren

Soren,

This is a bug I encountered recently in my investigations with log scales. While most projections are handling this properly, there are some cases where this problem sneaks in. I have not been able to figure out how to permanently address this issue.

For reference, the similiar issue is when zooming in on polar plots with the radial axis in log scale.

Ben Root

4

Thanks for info Goyo and Ben!

2011/3/11 Benjamin Root <ben.root@…1304…>

···

2011/3/10 Søren Nielsen <soren.skou.nielsen@…287…>

Hi,

When I do an errorbar plot (a.errorbar(), a = axis) with negative values and then try to change the yscale to log (a.set_yscale(‘log’)) matplotlib crashes with:

Traceback (most recent call last):

File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )

File “/home/specuser/new_workspace/TestDriven/src/RAWPlot.py”, line 371, in plotSASM

line, ec, el = a.errorbar(sasm.q[q_min:q_max], sasm.i[q_min:q_max], sasm.err[q_min:q_max], picker = 3, label = legend_label, **kwargs)

File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 4872, in errorbar

barcols.append( self.vlines(x, lower, upper, **lines_kw) )

File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 3302, in vlines
self.autoscale_view()
File “/usr/lib64/python2.6/site-packages/matplotlib/axes.py”, line 1627, in autoscale_view

YL = self.yaxis.get_major_locator().view_limits(y0, y1)

File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1119, in view_limits
if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base)

File “/usr/lib64/python2.6/site-packages/matplotlib/ticker.py”, line 1030, in is_decade
return lx==int(lx)
OverflowError: cannot convert float infinity to integer
Traceback (most recent call last):

File “/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 14636, in
lambda event: event.callable(*event.args, **event.kw) )

File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 1953, in addItem

newItem = ManipItemPanel(self.underpanel, sasm, font_colour = item_colour)

File “/home/specuser/new_workspace/TestDriven/src/RAW.py”, line 2353, in init
color = conv.to_rgb(self.sasm.line.get_mfc())

AttributeError: ‘NoneType’ object has no attribute ‘get_mfc’

I don’t think this should be the expected outcome… rather it should not plot values that are illegal/negative (i.e. ignore them).

Is there a way I can get around this without having to search through my data and remove points that are negative or NaN or INF when the yscale needs to be log? That would also show an incorrect curve since a line would be drawn across the points that were removed… It should rather be gaps in the line.

Thanks,
Soren

Soren,

This is a bug I encountered recently in my investigations with log scales. While most projections are handling this properly, there are some cases where this problem sneaks in. I have not been able to figure out how to permanently address this issue.

For reference, the similiar issue is when zooming in on polar plots with the radial axis in log scale.

Ben Root