Re: [Matplotlib-users] imshow for .png- low resultion
Yes the interpolation had to be set to nearest or bicubic or bilinear for
it to function properly!!
Thanks a lot!!
Asma
On Thu, Mar 6, 2014 at 4:48 AM, Pierre Haessig wrote:
> Le 05/03/2014 22:37, Asma Riyaz a écrit :
>
> img= mpimg.imread('/home/asmariyaz/Desktop/mytree.png')
> phyl_ax.imshow(img,interpolation='nearest')
>
> Ok, so here you could try replace 'nearest' by 'bilinear' or 'bicubic'. I
> believe those are the most common choices for image resampling (because
> when you plot an image and then save it, there is a resampling involved).
> (http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.imshow for
> the other options)
>
> Of course, it's also worth playing the dpi argument of savefig, as
> suggested by Eric.
>
> best,
> Pierre
>
>
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Re: [Matplotlib-users] imshow for .png- low resultion
Le 05/03/2014 22:37, Asma Riyaz a écrit :
> img= mpimg.imread('/home/asmariyaz/Desktop/mytree.png')
> phyl_ax.imshow(img,interpolation='nearest')
Ok, so here you could try replace 'nearest' by 'bilinear' or 'bicubic'.
I believe those are the most common choices for image resampling
(because when you plot an image and then save it, there is a resampling
involved).
(http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.imshow for
the other options)
Of course, it's also worth playing the dpi argument of savefig, as
suggested by Eric.
best,
Pierre
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Re: [Matplotlib-users] imshow for .png- low resultion
On 2014/03/05 11:37 AM, Asma Riyaz wrote:
> Sorry I somehow forgot to paste the imshow call to plot the .png
> image(pasted the entire code again), I am trying the different
> interpolation parameters in the mean time as suggested by Pierre
>
> data=np.array(full_len)
> cmap = mpl.cm.hot
> if outlier==0:
> threshold=1
> else:
> threshold=outlier-0.01
>
> fig = plt.figure(figsize=(25,25))
> plt.suptitle(file_handle.replace('.csv',''),fontsize=22)
> cmap.set_over('green')
> cmap.set_under('grey')
> gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
> ,width_ratios=[1,1,-2,2])
> gs.tight_layout(fig,)
> phyl_ax=plt.subplot(gs[0]) ##,frameon=False)##
> ht_ax=plt.subplot(gs[1],sharey=phyl_ax)
> ##gs.tight_layout(fig, rect=[1,1,2,2])
> ht_ax.set_xlim(0,35)
> ht_ax.set_ylim(0,35)
> ##ht_ax.grid(color='white',linestyle='-',linewidth=1)
> ##fig.subplots_adjust(hspace=0)
> cb_ax,kw =mpl.colorbar.make_axes(ht_ax, shrink=0.65)
>
> plt.setp(phyl_ax.get_xticklabels(),visible=False)
> plt.setp(phyl_ax.get_yticklabels(),visible=False)
> plt.setp(ht_ax.get_xticklabels(),visible=True)
> plt.setp(ht_ax.get_yticklabels(),visible=True)
> plt.setp(phyl_ax.get_xticklines(),visible=False)
> plt.setp(phyl_ax.get_yticklines(),visible=False)
> plt.setp(ht_ax.get_xticklines(),visible=True)
> plt.setp(ht_ax.get_yticklines(),visible=True)
>
>
> img = ht_ax.imshow(data, cmap=cmap,
> interpolation='none',vmax=threshold)
> cb = mpl.colorbar.ColorbarBase(ax=cb_ax,cmap=cmap,
> extend='neither',**kw)
> cb.cmap.set_over('green')
> ##image_file =
> cbook.get_sample_data('/home/asmariyaz/Desktop/mytree.png',asfileobj=False)
> ##image = plt.imread(image_file)
> img= mpimg.imread('/home/asmariyaz/Desktop/mytree.png')
> phyl_ax.imshow(img,interpolation='nearest')
>
> heatmap_file=fig.savefig('/home/asmariyaz/Desktop/heatmap/'+file_handle+'.pdf',bbox_inches='tight')
Try giving savefig a dpi kwarg to increase the resolution with which the
image is saved in the pdf? Turn off anti-aliasing when you make the png?
Eric
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Re: [Matplotlib-users] imshow for .png- low resultion
Sorry I somehow forgot to paste the imshow call to plot the .png
image(pasted the entire code again), I am trying the different
interpolation parameters in the mean time as suggested by Pierre
data=np.array(full_len)
cmap = mpl.cm.hot
if outlier==0:
threshold=1
else:
threshold=outlier-0.01
fig = plt.figure(figsize=(25,25))
plt.suptitle(file_handle.replace('.csv',''),fontsize=22)
cmap.set_over('green')
cmap.set_under('grey')
gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
,width_ratios=[1,1,-2,2])
gs.tight_layout(fig,)
phyl_ax=plt.subplot(gs[0]) ##,frameon=False)##
ht_ax=plt.subplot(gs[1],sharey=phyl_ax)
##gs.tight_layout(fig, rect=[1,1,2,2])
ht_ax.set_xlim(0,35)
ht_ax.set_ylim(0,35)
##ht_ax.grid(color='white',linestyle='-',linewidth=1)
##fig.subplots_adjust(hspace=0)
cb_ax,kw =mpl.colorbar.make_axes(ht_ax, shrink=0.65)
plt.setp(phyl_ax.get_xticklabels(),visible=False)
plt.setp(phyl_ax.get_yticklabels(),visible=False)
plt.setp(ht_ax.get_xticklabels(),visible=True)
plt.setp(ht_ax.get_yticklabels(),visible=True)
plt.setp(phyl_ax.get_xticklines(),visible=False)
plt.setp(phyl_ax.get_yticklines(),visible=False)
plt.setp(ht_ax.get_xticklines(),visible=True)
plt.setp(ht_ax.get_yticklines(),visible=True)
img = ht_ax.imshow(data, cmap=cmap, interpolation='none',vmax=threshold)
cb = mpl.colorbar.ColorbarBase(ax=cb_ax,cmap=cmap,
extend='neither',**kw)
cb.cmap.set_over('green')
##image_file =
cbook.get_sample_data('/home/asmariyaz/Desktop/mytree.png',asfileobj=False)
##image = plt.imread(image_file)
img= mpimg.imread('/home/asmariyaz/Desktop/mytree.png')
phyl_ax.imshow(img,interpolation='nearest')
heatmap_file=fig.savefig('/home/asmariyaz/Desktop/heatmap/'+file_handle+'.pdf',bbox_inches='tight')
On Wed, Mar 5, 2014 at 3:27 PM, Pierre Haessig wrote:
> Hi Asma,
> Le 05/03/2014 21:19, Asma Riyaz a écrit :
>
> I am trying to merge a heat map(matplotlib) with a tree(.png), but the
> .png does not plot as needed or for that matter cannot be seen easily. Here
> is my code:
>
> ### CODE
> []
>
>img = ht_ax.imshow(data, cmap=cmap, interpolation='none',vmax=threshold)
>[]
>
> How can I make the resolution of the .png image better OR for that
> matter is there a better solution to merge these together?
>
> I see the imshow call to plot the matrix but not the one you use to
> plot the png image. Could it be that the poor image rendering is due to a
> bad choice for the interpolation param ?
>
> best,
> Pierre
>
>
> --
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries. Built-in WAN optimization and
> the
> freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: [Matplotlib-users] imshow for .png- low resultion
Hi Asma, Le 05/03/2014 21:19, Asma Riyaz a écrit : I am trying to merge a heat map(matplotlib) with a tree(.png), but the .png does not plot as needed or for that matter cannot be seen easily. Here is my code: ### CODE [] img = ht_ax.imshow(data, cmap=cmap, interpolation='none',vmax=threshold) [] How can I make the resolution of the .png image better OR for that matter is there a better solution to merge these together? I see the imshow call to plot the matrix but not the one you use to plot the png image. Could it be that the poor image rendering is due to a bad choice for the interpolation param ? best, Pierre -- Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] imshow for .png- low resultion
Thank you for replying!!
The tree I generate is not based on clustering of matrices but rather on
sequence data and hence the tree generation is different in this case. I am
still looking into the seaborn project if it can lead me anywhere.
Thanks
Asma
On Wed, Mar 5, 2014 at 3:34 PM, Paul Hobson wrote:
> Olga Botnivik is doing some work with these types of figures in her fork
> of the seaborn project.
> Example here: http://nbviewer.ipython.org/gist/olgabot/8341784
> Link to the PR in github: https://github.com/mwaskom/seaborn/pull/73
>
> Those might be a good place to start.
>
>
>
> On Wed, Mar 5, 2014 at 12:19 PM, Asma Riyaz wrote:
>
>> Hi
>> I am trying to merge a heat map(matplotlib) with a tree(.png), but the
>> .png does not plot as needed or for that matter cannot be seen easily. Here
>> is my code:
>>
>> ### CODE
>> cmap = mpl.cm.hot
>> if outlier==0:
>>threshold=1
>> else:
>>threshold=outlier-0.01
>>
>> fig = plt.figure(figsize=(25,25))
>> plt.suptitle(file_handle.replace('.csv',''),fontsize=22)
>> cmap.set_over('green')
>> cmap.set_under('grey')
>> gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
>> ,width_ratios=[1,1,-2,2])
>> phyl_ax=plt.subplot(gs[0],frameon=False)
>> ht_ax=plt.subplot(gs[1])
>> ##gs.tight_layout(fig, rect=[1,1,2,2])
>> ht_ax.set_xlim(0,35)
>> ht_ax.set_ylim(0,35)
>> ##ht_ax.grid(color='white',linestyle='-',linewidth=1)
>> fig.subplots_adjust(hspace=0)
>> cb_ax,kw =mpl.colorbar.make_axes(ht_ax, shrink=0.65)
>>
>>
>> plt.setp(phyl_ax.get_xticklabels(),visible=False)
>> plt.setp(phyl_ax.get_yticklabels(),visible=False)
>> plt.setp(ht_ax.get_xticklabels(),visible=True)
>> plt.setp(ht_ax.get_yticklabels(),visible=True)
>> plt.setp(phyl_ax.get_xticklines(),visible=False)
>> plt.setp(phyl_ax.get_yticklines(),visible=False)
>> plt.setp(ht_ax.get_xticklines(),visible=True)
>> plt.setp(ht_ax.get_yticklines(),visible=True)
>>
>>
>> img = ht_ax.imshow(data, cmap=cmap,
>> interpolation='none',vmax=threshold)
>> cb = mpl.colorbar.ColorbarBase(ax=cb_ax,cmap=cmap,
>> extend='neither',**kw)
>> cb.cmap.set_over('green')
>> image_file =
>> cbook.get_sample_data('/home/asmariyaz/Desktop/mytree.png',asfileobj=False)
>> image = plt.imread(image_file)
>>
>> How can I make the resolution of the .png image better OR for that matter
>> is there a better solution to merge these together?
>>
>> I am attaching the plot I am getting with this code- (WrongTree.pdf)
>>
>> Thanks
>> Asma
>>
>>
>> --
>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>> Perforce.
>> With Perforce, you get hassle-free workflows. Merge that actually works.
>> Faster operations. Version large binaries. Built-in WAN optimization and
>> the
>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>> ___
>> Matplotlib-users mailing list
>> Matplotlib-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>
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Re: [Matplotlib-users] imshow for .png- low resultion
Olga Botnivik is doing some work with these types of figures in her fork of
the seaborn project.
Example here: http://nbviewer.ipython.org/gist/olgabot/8341784
Link to the PR in github: https://github.com/mwaskom/seaborn/pull/73
Those might be a good place to start.
On Wed, Mar 5, 2014 at 12:19 PM, Asma Riyaz wrote:
> Hi
> I am trying to merge a heat map(matplotlib) with a tree(.png), but the
> .png does not plot as needed or for that matter cannot be seen easily. Here
> is my code:
>
> ### CODE
> cmap = mpl.cm.hot
> if outlier==0:
>threshold=1
> else:
>threshold=outlier-0.01
>
> fig = plt.figure(figsize=(25,25))
> plt.suptitle(file_handle.replace('.csv',''),fontsize=22)
> cmap.set_over('green')
> cmap.set_under('grey')
> gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
> ,width_ratios=[1,1,-2,2])
> phyl_ax=plt.subplot(gs[0],frameon=False)
> ht_ax=plt.subplot(gs[1])
> ##gs.tight_layout(fig, rect=[1,1,2,2])
> ht_ax.set_xlim(0,35)
> ht_ax.set_ylim(0,35)
> ##ht_ax.grid(color='white',linestyle='-',linewidth=1)
> fig.subplots_adjust(hspace=0)
> cb_ax,kw =mpl.colorbar.make_axes(ht_ax, shrink=0.65)
>
>
> plt.setp(phyl_ax.get_xticklabels(),visible=False)
> plt.setp(phyl_ax.get_yticklabels(),visible=False)
> plt.setp(ht_ax.get_xticklabels(),visible=True)
> plt.setp(ht_ax.get_yticklabels(),visible=True)
> plt.setp(phyl_ax.get_xticklines(),visible=False)
> plt.setp(phyl_ax.get_yticklines(),visible=False)
> plt.setp(ht_ax.get_xticklines(),visible=True)
> plt.setp(ht_ax.get_yticklines(),visible=True)
>
>
> img = ht_ax.imshow(data, cmap=cmap,
> interpolation='none',vmax=threshold)
> cb = mpl.colorbar.ColorbarBase(ax=cb_ax,cmap=cmap,
> extend='neither',**kw)
> cb.cmap.set_over('green')
> image_file =
> cbook.get_sample_data('/home/asmariyaz/Desktop/mytree.png',asfileobj=False)
> image = plt.imread(image_file)
>
> How can I make the resolution of the .png image better OR for that matter
> is there a better solution to merge these together?
>
> I am attaching the plot I am getting with this code- (WrongTree.pdf)
>
> Thanks
> Asma
>
>
> --
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries. Built-in WAN optimization and
> the
> freedom to use Git, Perforce or both. Make the move to Perforce.
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[Matplotlib-users] imshow for .png- low resultion
Hi
I am trying to merge a heat map(matplotlib) with a tree(.png), but the .png
does not plot as needed or for that matter cannot be seen easily. Here is
my code:
### CODE
cmap = mpl.cm.hot
if outlier==0:
threshold=1
else:
threshold=outlier-0.01
fig = plt.figure(figsize=(25,25))
plt.suptitle(file_handle.replace('.csv',''),fontsize=22)
cmap.set_over('green')
cmap.set_under('grey')
gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
,width_ratios=[1,1,-2,2])
phyl_ax=plt.subplot(gs[0],frameon=False)
ht_ax=plt.subplot(gs[1])
##gs.tight_layout(fig, rect=[1,1,2,2])
ht_ax.set_xlim(0,35)
ht_ax.set_ylim(0,35)
##ht_ax.grid(color='white',linestyle='-',linewidth=1)
fig.subplots_adjust(hspace=0)
cb_ax,kw =mpl.colorbar.make_axes(ht_ax, shrink=0.65)
plt.setp(phyl_ax.get_xticklabels(),visible=False)
plt.setp(phyl_ax.get_yticklabels(),visible=False)
plt.setp(ht_ax.get_xticklabels(),visible=True)
plt.setp(ht_ax.get_yticklabels(),visible=True)
plt.setp(phyl_ax.get_xticklines(),visible=False)
plt.setp(phyl_ax.get_yticklines(),visible=False)
plt.setp(ht_ax.get_xticklines(),visible=True)
plt.setp(ht_ax.get_yticklines(),visible=True)
img = ht_ax.imshow(data, cmap=cmap, interpolation='none',vmax=threshold)
cb = mpl.colorbar.ColorbarBase(ax=cb_ax,cmap=cmap,
extend='neither',**kw)
cb.cmap.set_over('green')
image_file =
cbook.get_sample_data('/home/asmariyaz/Desktop/mytree.png',asfileobj=False)
image = plt.imread(image_file)
How can I make the resolution of the .png image better OR for that matter
is there a better solution to merge these together?
I am attaching the plot I am getting with this code- (WrongTree.pdf)
Thanks
Asma
WrongTree.pdf
Description: Adobe PDF document
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