From joeyajames at yahoo.com Mon Feb 1 01:16:38 2016 From: joeyajames at yahoo.com (joeyajames) Date: Sun, 31 Jan 2016 23:16:38 -0700 (MST) Subject: [Matplotlib-users] Heatmap Continent Transparency Message-ID: <1454307398100-46707.post@n5.nabble.com> I need to make the land areas transparent in my heatmaps because I am overlaying them on a Google map, as you can see here, http://pmc.ucsc.edu/~joeyajames/ I tried m.fillcontinents(color='white', alpha=0.0), but that doesn't work. Without the fillcontinents() statement the land is red, and changing the alpha only controls how much red shows through the white. Somehow I think I need to mask out the data points on the land so the heatmap doesn't make them red. Any tips? m = Basemap(llcrnrlon=MIN_LON, llcrnrlat=MIN_LAT, urcrnrlon=MAX_LON, urcrnrlat=MAX_LAT, resolution='l',area_thresh=10000.,projection='merc',lat_ts=20) lons, lats = np.meshgrid(lons1,lats1) nlats = 3*topoin.shape[0] nlons = 3*topoin.shape[1] lons = np.linspace(MIN_LON, MAX_LON, nlons) lats = np.linspace(MIN_LAT, MAX_LAT, nlats) lons, lats = np.meshgrid(lons, lats) x, y = m(lons, lats) topo = interp(topoin,lons1,lats1,lons,lats,order=1) minval, maxval = get_range2(topo) m.pcolormesh(x,y,topo,cmap=plt.cm.jet,vmin=minval,vmax=maxval) m.colorbar() # m.fillcontinents(color='white') m.drawcountries() m.drawcoastlines() plt.show() fig.savefig(filename, bbox_inches='tight', transparent=True) -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Heatmap-Continent-Transparency-tp46707.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 12:36:22 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 10:36:22 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> Message-ID: <1454607382031-46709.post@n5.nabble.com> Paul, Thanks for the reply, since my last post I've been working on this lots and have a working script. Pictures below, took me a while to get it working but it does. the main issue I have with it is that as you can see from the pictures when the time periods for a day are stacked for some reason the are all on a slant (presumably time related) Is there a way to straighten it all up ? as in the script below it now receives ['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] for each event, the basics are there but its not very pretty yet. Im still trying to figure out how I got it working quite an achievement for me if i#m honest. code def createGraph(self): #data appears like so: #date,init time,end time,elapsed time #3/6/2013,4:30:00,8:45:00,4:15:00 try: data = np.array(self.graphList1) #print data[1] #['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] day = data[:,0] hour1 = data[:,1] hour2 = data[:,2] hour3 = data[:,3] inittime = [a+' '+b for a,b in zip(day, hour1)] elapsedtime = [a+' '+b for a,b in zip(day, hour3)] #print inittime # 3/6/2013 4:30:00 except Exception, e: print e #from [1], " I gave up after trying a few different ways, and resorted to a very easy workaround. # Plot the times as integer minutes : 0 being midnight, 60 = 1am ... which is 24hr * 60. " def dt2m(dt): return (dt.hour*60) + dt.minute print inittime[0] inittime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M') for foo in inittime] elapsedtime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M:%S') for foo in elapsedtime] #os.remove('chart.csv') # [1] "Then format the Y axis as Hour:Minute using a custom formatter:" def m2hm(x, i): h = int(x/60) m = int(x%60) return '%(h)02d:%(m)02d' % {'h':h,'m':m} inittime_mins = [dt2m(foo) for foo in inittime] elaptime_mins = [dt2m(foo) for foo in elapsedtime] #heights = [60,120,240] #print inittime_mins fig = plt.figure(figsize=(12,7)) #figsize in inches ax = fig.add_subplot(1, 1, 1) ax.bar(inittime,elaptime_mins,bottom=inittime_mins) plt.xticks(rotation='45') # matplotlib date format object hfmt = dates.DateFormatter('%b %d') ax.xaxis.set_major_formatter(hfmt) ax.xaxis.set_major_locator(plt.MultipleLocator(1.0)) #a tick mark a day ax.set_ylim([20*60, 5*60]) ax.yaxis.set_major_formatter(ff(m2hm)) ax.yaxis.set_major_locator(plt.MultipleLocator(60)) #a tick mark an hour plt.subplots_adjust (left = 0.06, bottom = 0.10, right = 0.97, top = 0.97, wspace = 0.20, hspace = 0.20) plt.show()code -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46709.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 12:42:11 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 10:42:11 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1453938279802-46683.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> Message-ID: <1454607731208-46710.post@n5.nabble.com> Paul, Thanks for the reply, since my last post I've been working on this lots and have a working script. Pictures below, took me a while to get it working but it does. the main issue I have with it is that as you can see from the pictures when the time periods for a day are stacked for some reason the are all on a slant (presumably time related) Is there a way to straighten it all up ? as in the script below it now receives ['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] for each event, the basics are there but its not very pretty yet. Im still trying to figure out how I got it working quite an achievement for me if i#m honest. code def createGraph(self): #data appears like so: #date,init time,end time,elapsed time #3/6/2013,4:30:00,8:45:00,4:15:00 try: data = np.array(self.graphList1) #print data[1] #['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] day = data[:,0] hour1 = data[:,1] hour2 = data[:,2] hour3 = data[:,3] inittime = [a+' '+b for a,b in zip(day, hour1)] elapsedtime = [a+' '+b for a,b in zip(day, hour3)] #print inittime # 3/6/2013 4:30:00 except Exception, e: print e #from [1], " I gave up after trying a few different ways, and resorted to a very easy workaround. # Plot the times as integer minutes : 0 being midnight, 60 = 1am ... which is 24hr * 60. " def dt2m(dt): return (dt.hour*60) + dt.minute print inittime[0] inittime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M') for foo in inittime] elapsedtime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M:%S') for foo in elapsedtime] #os.remove('chart.csv') # [1] "Then format the Y axis as Hour:Minute using a custom formatter:" def m2hm(x, i): h = int(x/60) m = int(x%60) return '%(h)02d:%(m)02d' % {'h':h,'m':m} inittime_mins = [dt2m(foo) for foo in inittime] elaptime_mins = [dt2m(foo) for foo in elapsedtime] #heights = [60,120,240] #print inittime_mins fig = plt.figure(figsize=(12,7)) #figsize in inches ax = fig.add_subplot(1, 1, 1) ax.bar(inittime,elaptime_mins,bottom=inittime_mins) plt.xticks(rotation='45') # matplotlib date format object hfmt = dates.DateFormatter('%b %d') ax.xaxis.set_major_formatter(hfmt) ax.xaxis.set_major_locator(plt.MultipleLocator(1.0)) #a tick mark a day ax.set_ylim([20*60, 5*60]) ax.yaxis.set_major_formatter(ff(m2hm)) ax.yaxis.set_major_locator(plt.MultipleLocator(60)) #a tick mark an hour plt.subplots_adjust (left = 0.06, bottom = 0.10, right = 0.97, top = 0.97, wspace = 0.20, hspace = 0.20) plt.show()code -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46710.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 12:57:47 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 10:57:47 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> Message-ID: <1454608667746-46711.post@n5.nabble.com> Paul, Thanks for the reply, since my last post I've been working on this lots and have a working script. Pictures below, took me a while to get it working but it does. the main issue I have with it is that as you can see from the pictures when the time periods for a day are stacked for some reason the are all on a slant (presumably time related) Is there a way to straighten it all up ? as in the script below it now receives ['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] for each event, the basics are there but its not very pretty yet. Im still trying to figure out how I got it working quite an achievement for me if i#m honest. code def createGraph(self): #data appears like so: #date,init time,end time,elapsed time #3/6/2013,4:30:00,8:45:00,4:15:00 try: data = np.array(self.graphList1) #print data[1] #['3/6/2013' '11:30:00' '14:30:00' '3:00:00'] day = data[:,0] hour1 = data[:,1] hour2 = data[:,2] hour3 = data[:,3] inittime = [a+' '+b for a,b in zip(day, hour1)] elapsedtime = [a+' '+b for a,b in zip(day, hour3)] #print inittime # 3/6/2013 4:30:00 except Exception, e: print e #from [1], " I gave up after trying a few different ways, and resorted to a very easy workaround. # Plot the times as integer minutes : 0 being midnight, 60 = 1am ... which is 24hr * 60. " def dt2m(dt): return (dt.hour*60) + dt.minute print inittime[0] inittime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M') for foo in inittime] elapsedtime = [datetime.datetime.strptime(foo,'%d/%m/%Y %H:%M:%S') for foo in elapsedtime] #os.remove('chart.csv') # [1] "Then format the Y axis as Hour:Minute using a custom formatter:" def m2hm(x, i): h = int(x/60) m = int(x%60) return '%(h)02d:%(m)02d' % {'h':h,'m':m} inittime_mins = [dt2m(foo) for foo in inittime] elaptime_mins = [dt2m(foo) for foo in elapsedtime] #heights = [60,120,240] #print inittime_mins fig = plt.figure(figsize=(12,7)) #figsize in inches ax = fig.add_subplot(1, 1, 1) ax.bar(inittime,elaptime_mins,bottom=inittime_mins) plt.xticks(rotation='45') # matplotlib date format object hfmt = dates.DateFormatter('%b %d') ax.xaxis.set_major_formatter(hfmt) ax.xaxis.set_major_locator(plt.MultipleLocator(1.0)) #a tick mark a day ax.set_ylim([20*60, 5*60]) ax.yaxis.set_major_formatter(ff(m2hm)) ax.yaxis.set_major_locator(plt.MultipleLocator(60)) #a tick mark an hour plt.subplots_adjust (left = 0.06, bottom = 0.10, right = 0.97, top = 0.97, wspace = 0.20, hspace = 0.20) plt.show()code -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46711.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 13:18:14 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 11:18:14 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> Message-ID: <1454609894565-46712.post@n5.nabble.com> Paul, Sorry for the delay, I had trouble getting the original post accepted .... I replied on the 29th of Jan. Since the previous post I have found some code that almost does what I wanted but as always when you get a little more of something you lost it somewhere else. what I have now is displaying - the code to create the graph is - code def plot_durations(self,starts, stops, ax=None, **kwargs): if ax is None: ax = plt.gca() # Make the default alignment center, unless specified otherwise kwargs['align'] = kwargs.get('align', 'center') # Convert things to matplotlib's internal date format... starts, stops = mpl.dates.date2num(starts), mpl.dates.date2num(stops) # Break things into start days and start times start_times = starts % 1 start_days = starts - start_times durations = stops - starts start_times += int(starts[0]) # So that we have a valid date... # Plot the bars artist = ax.bar(start_days, durations, bottom=start_times, **kwargs) # Tell matplotlib to treat the axes as dates... ax.xaxis_date() ax.yaxis_date() ax.figure.autofmt_xdate() plt.show() code Issues or things id like to or am trying to change :- The code is the same for both graphs but one shows times for the x axis and not date (must be due to the data range) id like it to show only dates on the x axis but also every date, not missing any .. as the previous version did. I would like the y axis to display time am at the top pm at the bottom as the previous version did. there are a few other things but one step at a time I guess, I have tried to copy lines from the older version to the new one but without success. Cheers Stevo -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46712.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 15:49:48 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 13:49:48 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1454609894565-46712.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> <1454609894565-46712.post@n5.nabble.com> Message-ID: <1454618988786-46713.post@n5.nabble.com> OK first step forward ..... inverted the y axis with ... 'plt.gca().invert_yaxis()' -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46713.html Sent from the matplotlib - users mailing list archive at Nabble.com. From ben.v.root at gmail.com Thu Feb 4 15:57:22 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Thu, 4 Feb 2016 15:57:22 -0500 Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1454618988786-46713.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> <1454609894565-46712.post@n5.nabble.com> <1454618988786-46713.post@n5.nabble.com> Message-ID: better: `ax.invert_yaxis()`? You have no guarantee that `plt.gca()` is the same as the `ax` parameter that you have in your function. Ben Root On Thu, Feb 4, 2016 at 3:49 PM, Stevo wrote: > OK first step forward ..... inverted the y axis with ... > 'plt.gca().invert_yaxis()' > > > > -- > View this message in context: > http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46713.html > Sent from the matplotlib - users mailing list archive at Nabble.com. > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stm6386 at gmail.com Thu Feb 4 16:58:04 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 14:58:04 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> <1454609894565-46712.post@n5.nabble.com> <1454618988786-46713.post@n5.nabble.com> Message-ID: <1454623084285-46715.post@n5.nabble.com> Ben, Please for give me for not being experienced enough in python to understand the significance of the difference of that but I have changed it .. thank you. Loving Python Stevo -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46715.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Thu Feb 4 17:00:12 2016 From: stm6386 at gmail.com (Stevo) Date: Thu, 4 Feb 2016 15:00:12 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> <1454609894565-46712.post@n5.nabble.com> <1454618988786-46713.post@n5.nabble.com> Message-ID: <1454623212439-46716.post@n5.nabble.com> Ben, Please for give me for not being experienced enough in python to understand the significance of the difference of that but I have changed it .. thank you. Loving Python Stevo -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46716.html Sent from the matplotlib - users mailing list archive at Nabble.com. From ben.v.root at gmail.com Thu Feb 4 17:16:18 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Thu, 4 Feb 2016 17:16:18 -0500 Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1454623212439-46716.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> <1453938279802-46683.post@n5.nabble.com> <1454609894565-46712.post@n5.nabble.com> <1454618988786-46713.post@n5.nabble.com> <1454623212439-46716.post@n5.nabble.com> Message-ID: Stevo, Don't worry, we all started from somewhere, but it is important to understand the distinction. This has nothing to do with python, by the way. `plt.gca()` returns the "current"/"active" axes object. Meanwhile, your function does its plotting on an axes object called "ax". These may or may not be the same thing -- you just simply don't know. So, your function should continue to perform its plotting commands on the "ax" variable, not on the result from `plt.gca()`. Note though, it is perfectly valid what you have in the beginning of the function what called `plt.gca()` if "ax" was not supplied by the user. But you should continue to use "ax" throughout the function so that all actions happen to the same variable. I hope that makes it clearer. Ben Root On Thu, Feb 4, 2016 at 5:00 PM, Stevo wrote: > Ben, > > Please for give me for not being experienced enough in python to understand > the significance of the difference of that but I have changed it .. thank > you. > > Loving Python > Stevo > > > > -- > View this message in context: > http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46716.html > Sent from the matplotlib - users mailing list archive at Nabble.com. > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stm6386 at gmail.com Fri Feb 5 13:53:56 2016 From: stm6386 at gmail.com (Stevo) Date: Fri, 5 Feb 2016 11:53:56 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1453853256420-46682.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> Message-ID: <1454698436593-46719.post@n5.nabble.com> Guys, This is where I am now - code def plot_durations(self,starts, stops, ax , **kwargs): if ax is None: ax = plt.gca() # Make the default alignment center, unless specified otherwise kwargs['align'] = kwargs.get('align', 'center') # Convert things to matplotlib's internal date format... starts, stops = mpl.dates.date2num(starts), mpl.dates.date2num(stops) # Break things into start days and start times start_times = starts % 1 start_days = starts - start_times durations = stops - starts start_times += int(starts[0]) # So that we have a valid date... # Plot the bars artist = ax.bar(start_days, durations, bottom=start_times, **kwargs) # Tell matplotlib to treat the axes as dates... hfmt = dates.DateFormatter('%b %d') ax.xaxis.set_major_formatter(hfmt) ax.xaxis.set_major_locator(plt.MultipleLocator(1.0)) #a tick mark a day ax.yaxis_date() ax.figure.autofmt_xdate() ax.invert_yaxis() plt.subplots_adjust (left = 0.1, bottom = 0.10, right = 0.97, top = 0.97, wspace = 0.20, hspace = 0.2) plt.show() code But for some reason I get inconsistent results for the y axis ..... I would prefer just hh:mm format if I could set it but have no idea why it would the extra 0's ... the script wasnt restarted or anything just another set of data used, the data looked identical in each case so I have no idea what the change is caused by .... selecting and reselecting data just gave the same results. I could show the whole script if it helps but it gets quite complex. Just learning and loving Python Stevo -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46719.html Sent from the matplotlib - users mailing list archive at Nabble.com. From pmhobson at gmail.com Sat Feb 6 00:57:51 2016 From: pmhobson at gmail.com (Paul Hobson) Date: Fri, 5 Feb 2016 21:57:51 -0800 Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: <1454698436593-46719.post@n5.nabble.com> References: <1453853256420-46682.post@n5.nabble.com> <1454698436593-46719.post@n5.nabble.com> Message-ID: Looks like you should set the y-formatter in a similar fashion as you do the the x-formatter: hrmin_fmt = dates.DateFormatter('%H %M') ax.yaxis.set_major_formatter(hrmin_fmt) On Fri, Feb 5, 2016 at 10:53 AM, Stevo wrote: > Guys, > This is where I am now - > code > def plot_durations(self,starts, stops, ax , **kwargs): > if ax is None: > ax = plt.gca() > # Make the default alignment center, unless specified otherwise > kwargs['align'] = kwargs.get('align', 'center') > > # Convert things to matplotlib's internal date format... > starts, stops = mpl.dates.date2num(starts), > mpl.dates.date2num(stops) > > # Break things into start days and start times > start_times = starts % 1 > start_days = starts - start_times > durations = stops - starts > start_times += int(starts[0]) # So that we have a valid date... > > # Plot the bars > artist = ax.bar(start_days, durations, bottom=start_times, > **kwargs) > > # Tell matplotlib to treat the axes as dates... > hfmt = dates.DateFormatter('%b %d') > ax.xaxis.set_major_formatter(hfmt) > ax.xaxis.set_major_locator(plt.MultipleLocator(1.0)) #a tick mark a > day > ax.yaxis_date() > ax.figure.autofmt_xdate() > ax.invert_yaxis() > plt.subplots_adjust (left = 0.1, bottom = 0.10, right = 0.97, top = > 0.97, wspace = 0.20, hspace = 0.2) > plt.show() > code > > But for some reason I get inconsistent results for the y axis ..... > > > I would prefer just hh:mm format if I could set it but have no idea why it > would the extra 0's ... the script wasnt restarted or anything just another > set of data used, the data looked identical in each case so I have no idea > what the change is caused by .... selecting and reselecting data just gave > the same results. > I could show the whole script if it helps but it gets quite complex. > > Just learning and loving Python > Stevo > > > > -- > View this message in context: > http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46719.html > Sent from the matplotlib - users mailing list archive at Nabble.com. > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From efiring at hawaii.edu Sat Feb 6 01:02:47 2016 From: efiring at hawaii.edu (Eric Firing) Date: Fri, 5 Feb 2016 20:02:47 -1000 Subject: [Matplotlib-users] Editing legend labels In-Reply-To: References: Message-ID: <56B58C87.9040902@hawaii.edu> On 2016/01/26 1:24 AM, Lorenzo De Leo wrote: > Hello, > > I have a problem with the way the legend labels are handled, certainly > due to my poor knowledge of matplotlib internals. > > Here an example (matplotlib-1.4.3, py-2.7): > > In [1]: import matplotlib.pyplot as plt > > In [2]: plt.plot([1,2,3], label='A') > Out[2]: [] > > In [3]: plt.plot([2,3,4], label='B') > Out[3]: [] > > In [4]: ax = plt.gca() > > In [5]: l = ax.get_legend_handles_labels() > > In [6]: l > Out[6]: > ([, > ], > [u'A', u'B']) > > In [7]: plt.legend(['C', 'D']) ### This correctly modifies the legend > to show 'C' and 'D', but then ... > Out[7]: > > In [10]: l = ax.get_legend_handles_labels() > > In [11]: l > Out[11]: > ([, > ], > [u'A', u'B']) > > At this point I have no idea how to retrieve the list of shown labels, > i.e. ['C', 'D']. > What am I missing? What other method should I use? You can do this: leg = plt.legend(['C', 'D']) labels = [t.get_text() for t in leg.get_texts()] Eric > > Thanks in advance > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > From stm6386 at gmail.com Sat Feb 6 07:52:50 2016 From: stm6386 at gmail.com (Stevo) Date: Sat, 6 Feb 2016 05:52:50 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1454698436593-46719.post@n5.nabble.com> Message-ID: <1454763170081-46722.post@n5.nabble.com> Paul, That does it perfectly, I had tried something similar myself but wasnt sure what I was doing and obviously got it wrong. Works perfect now. Very thankful Stevo -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46722.html Sent from the matplotlib - users mailing list archive at Nabble.com. From stm6386 at gmail.com Sun Feb 7 05:42:53 2016 From: stm6386 at gmail.com (Stevo) Date: Sun, 7 Feb 2016 03:42:53 -0700 (MST) Subject: [Matplotlib-users] Totaly new to matplotlib In-Reply-To: References: <1453853256420-46682.post@n5.nabble.com> <1454698436593-46719.post@n5.nabble.com> Message-ID: <1454841773004-46723.post@n5.nabble.com> One thing I have noticed that seems very very odd to me is that for no apparent reason I get one odd darker blue coloured line on some of the graphs. weird ! -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Totaly-new-to-matplotlib-tp46682p46723.html Sent from the matplotlib - users mailing list archive at Nabble.com. From ilja.j.honkonen at nasa.gov Wed Feb 10 12:06:40 2016 From: ilja.j.honkonen at nasa.gov (Ilja Honkonen) Date: Wed, 10 Feb 2016 12:06:40 -0500 Subject: [Matplotlib-users] How to plot tick values in-place? Message-ID: <56BB6E20.3050301@nasa.gov> Hello I didn't find an answer with google or stackoverflow, maybe someone here can help? The code: import matplotlib.pyplot as plot plot.plot([0, 1e-9, 0, -1e-9]) plot.show() produces a plot in which y ticks are -1, -0.5, 0, 0.5, 1 and their scaling is plotted elsewhere, how do I force matplotlib to plot the tics in-place as -1e-9, -0.5-e9... so I don't have to search other parts of the plot for potential corrections to tick values? Thanks! Ilja From ben.v.root at gmail.com Wed Feb 10 12:52:23 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Wed, 10 Feb 2016 12:52:23 -0500 Subject: [Matplotlib-users] How to plot tick values in-place? In-Reply-To: <56BB6E20.3050301@nasa.gov> References: <56BB6E20.3050301@nasa.gov> Message-ID: I think setting the rcParam 'axes.formatter.useoffset' to False prior to any plotting would do the trick. plot.rcParams['axes.formatter.useoffset'] = False Untested, though. Ben Root On Wed, Feb 10, 2016 at 12:06 PM, Ilja Honkonen wrote: > Hello > I didn't find an answer with google or stackoverflow, maybe someone here > can help? The code: > > import matplotlib.pyplot as plot > plot.plot([0, 1e-9, 0, -1e-9]) > plot.show() > > produces a plot in which y ticks are -1, -0.5, 0, 0.5, 1 and their scaling > is plotted elsewhere, how do I force matplotlib to plot the tics in-place > as -1e-9, -0.5-e9... so I don't have to search other parts of the plot for > potential corrections to tick values? Thanks! > Ilja > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilja.j.honkonen at nasa.gov Wed Feb 10 13:21:24 2016 From: ilja.j.honkonen at nasa.gov (Ilja Honkonen) Date: Wed, 10 Feb 2016 13:21:24 -0500 Subject: [Matplotlib-users] How to plot tick values in-place? In-Reply-To: References: <56BB6E20.3050301@nasa.gov> Message-ID: <56BB7FA4.2000805@nasa.gov> > I think setting the rcParam '|axes.formatter.useoffset' |to False prior > to any plotting would do the trick.| > |plot.rcParams['axes.formatter.useoffset'] = False My matplotlib.__version__ == '1.1.1' doesn't have that neither in matplotlib nor in plot: >>> matplotlib.rcParams['axes.formatter.useoffset'] = False Traceback (most recent call last): File "", line 1, in File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 660, in __setitem__ See rcParams.keys() for a list of valid parameters.' % (key,)) KeyError: 'axes.formatter.useoffset is not a valid rc parameter.See rcParams.keys() for a list of valid parameters.' >>> matplotlib.pyplot.rcParams['axes.formatter.useoffset'] = False Traceback (most recent call last): File "", line 1, in File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/__init__.py", line 660, in __setitem__ See rcParams.keys() for a list of valid parameters.' % (key,)) KeyError: 'axes.formatter.useoffset is not a valid rc parameter.See rcParams.keys() for a list of valid parameters.' Also I did find this: plot.ticklabel_format(useOffset = False) which looks like what you suggest but that only removes offset from ticks not scaling. Thanks Ilja From bachir_bac at yahoo.com Fri Feb 12 14:54:08 2016 From: bachir_bac at yahoo.com (Bachir Bachir) Date: Fri, 12 Feb 2016 19:54:08 +0000 (UTC) Subject: [Matplotlib-users] stem plot References: <1299768174.3271262.1455306848586.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1299768174.3271262.1455306848586.JavaMail.yahoo@mail.yahoo.com> Dear all,Using stem plot how i can display a serie of values (x,y) but when the y value is less than a specific toterance the display color is green otherwise the color is redthanks much for the helpBachir -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmhobson at gmail.com Fri Feb 12 15:09:29 2016 From: pmhobson at gmail.com (Paul Hobson) Date: Fri, 12 Feb 2016 12:09:29 -0800 Subject: [Matplotlib-users] stem plot In-Reply-To: <1299768174.3271262.1455306848586.JavaMail.yahoo@mail.yahoo.com> References: <1299768174.3271262.1455306848586.JavaMail.yahoo.ref@mail.yahoo.com> <1299768174.3271262.1455306848586.JavaMail.yahoo@mail.yahoo.com> Message-ID: Call to stem plot twice: once with your dataset that is above the threshold, and then again with the lower values. Similar to this: http://stackoverflow.com/questions/19917587/matplotlib-advanced-bar-plot/19919397#19919397 On Fri, Feb 12, 2016 at 11:54 AM, Bachir Bachir via Matplotlib-users < matplotlib-users at python.org> wrote: > Dear all, > Using stem plot how i can display a serie of values (x,y) but when the y > value is less than a specific toterance the display color is green > otherwise the color is red > thanks much for the help > Bachir > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bachir_bac at yahoo.com Fri Feb 12 15:37:10 2016 From: bachir_bac at yahoo.com (Bachir Bachir) Date: Fri, 12 Feb 2016 20:37:10 +0000 (UTC) Subject: [Matplotlib-users] stem plot In-Reply-To: References: Message-ID: <425453106.3186916.1455309430740.JavaMail.yahoo@mail.yahoo.com> ?I think only one call is enough, if you change the color ( green or red) depending on the tolerance value.?My case is little different , I want display all the values above the tolerance using red color and the all the rest using green. On Friday, February 12, 2016 9:09 PM, Paul Hobson wrote: Call to stem plot twice: once with your dataset that is above the threshold, and then again with the lower values. Similar to this:http://stackoverflow.com/questions/19917587/matplotlib-advanced-bar-plot/19919397#19919397 On Fri, Feb 12, 2016 at 11:54 AM, Bachir Bachir via Matplotlib-users wrote: Dear all,Using stem plot how i can display a serie of values (x,y) but when the y value is less than a specific toterance the display color is green otherwise the color is redthanks much for the helpBachir _______________________________________________ Matplotlib-users mailing list Matplotlib-users at python.org https://mail.python.org/mailman/listinfo/matplotlib-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ben.v.root at gmail.com Fri Feb 12 16:04:23 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Fri, 12 Feb 2016 16:04:23 -0500 Subject: [Matplotlib-users] stem plot In-Reply-To: <425453106.3186916.1455309430740.JavaMail.yahoo@mail.yahoo.com> References: <425453106.3186916.1455309430740.JavaMail.yahoo@mail.yahoo.com> Message-ID: Perhaps it is the cold weather that is messing up my reading comprehension, but I don't see how your case is different from what Paul described. Ben Root On Fri, Feb 12, 2016 at 3:37 PM, Bachir Bachir via Matplotlib-users < matplotlib-users at python.org> wrote: > I think only one call is enough, if you change the color ( green or red) > depending on the tolerance value. > My case is little different , I want display all the values above the > tolerance using red color and the all the rest using green. > > > > > On Friday, February 12, 2016 9:09 PM, Paul Hobson > wrote: > > > Call to stem plot twice: once with your dataset that is above the > threshold, and then again with the lower values. Similar to this: > > http://stackoverflow.com/questions/19917587/matplotlib-advanced-bar-plot/19919397#19919397 > > On Fri, Feb 12, 2016 at 11:54 AM, Bachir Bachir via Matplotlib-users < > matplotlib-users at python.org> wrote: > > Dear all, > Using stem plot how i can display a serie of values (x,y) but when the y > value is less than a specific toterance the display color is green > otherwise the color is red > thanks much for the help > Bachir > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > > > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bachir_bac at yahoo.com Fri Feb 12 16:57:46 2016 From: bachir_bac at yahoo.com (Bachir Bachir) Date: Fri, 12 Feb 2016 21:57:46 +0000 (UTC) Subject: [Matplotlib-users] stem plot In-Reply-To: References: Message-ID: <1708463040.3352772.1455314266868.JavaMail.yahoo@mail.yahoo.com> ?I want to display all the values above the tolerance using red color for example and the all the values bellow the tolerance using green color, what Paul discribed the colors are side by side an the bar have the same color?exactly i want to display from the tolerance to maximum value using red and from the tolerance to zero using green?i hope this time i am clear? On Friday, February 12, 2016 10:04 PM, Benjamin Root wrote: Perhaps it is the cold weather that is messing up my reading comprehension, but I don't see how your case is different from what Paul described. Ben Root On Fri, Feb 12, 2016 at 3:37 PM, Bachir Bachir via Matplotlib-users wrote: ?I think only one call is enough, if you change the color ( green or red) depending on the tolerance value.?My case is little different , I want display all the values above the tolerance using red color and the all the rest using green. On Friday, February 12, 2016 9:09 PM, Paul Hobson wrote: Call to stem plot twice: once with your dataset that is above the threshold, and then again with the lower values. Similar to this:http://stackoverflow.com/questions/19917587/matplotlib-advanced-bar-plot/19919397#19919397 On Fri, Feb 12, 2016 at 11:54 AM, Bachir Bachir via Matplotlib-users wrote: Dear all,Using stem plot how i can display a serie of values (x,y) but when the y value is less than a specific toterance the display color is green otherwise the color is redthanks much for the helpBachir _______________________________________________ Matplotlib-users mailing list Matplotlib-users at python.org https://mail.python.org/mailman/listinfo/matplotlib-users _______________________________________________ Matplotlib-users mailing list Matplotlib-users at python.org https://mail.python.org/mailman/listinfo/matplotlib-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nilsc.becker at gmail.com Sun Feb 14 08:52:57 2016 From: nilsc.becker at gmail.com (Nils Becker) Date: Sun, 14 Feb 2016 14:52:57 +0100 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation Message-ID: Hello everyone, as the direct observation of gravitational waves made its way round the world a few days ago, I was pleased to see that they (very probably) used matplotlib for their plots. They even used the new viridis colormap [1]. I could not confirm this directly for the plots in the paper but at least the data analysis stack at LIGO seems to be built partly on python. They provide scripts to reproduce the data analysis in python and use matplotlib to plot it [2]. In any case, maybe it's an idea to contact LIGO to confirm this and ask them if we could put the figure on the website gallery as a kind of "plot of honor" or something? I mean there is a chance that it's going to be the most famous plot done in matplotlib to this date. Cheers Nils [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 (page 2) [2] https://losc.ligo.org/software/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.hillairet at gmail.com Mon Feb 15 10:24:32 2016 From: julien.hillairet at gmail.com (Julien Hillairet) Date: Mon, 15 Feb 2016 16:24:32 +0100 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Hi, There is a Reddit Ask us Anything concerning the LIGO Scientific Collaboration, with a dedicated discussion on the use of Python (and Matplotlib): https://www.reddit.com/r/IAmA/comments/45g8qu/we_are_the_ligo_scientific_collaboration_and_we/czxnlux Regards, Julien 2016-02-14 14:52 GMT+01:00 Nils Becker : > Hello everyone, > > as the direct observation of gravitational waves made its way round the > world a few days ago, I was pleased to see that they (very probably) used > matplotlib for their plots. They even used the new viridis colormap [1]. > I could not confirm this directly for the plots in the paper but at least > the data analysis stack at LIGO seems to be built partly on python. They > provide scripts to reproduce the data analysis in python and use matplotlib > to plot it [2]. > > In any case, maybe it's an idea to contact LIGO to confirm this and ask > them if we could put the figure on the website gallery as a kind of "plot > of honor" or something? I mean there is a chance that it's going to be the > most famous plot done in matplotlib to this date. > > Cheers > Nils > > [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 > (page 2) > [2] https://losc.ligo.org/software/ > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tcaswell at gmail.com Tue Feb 16 00:18:59 2016 From: tcaswell at gmail.com (Thomas Caswell) Date: Tue, 16 Feb 2016 05:18:59 +0000 Subject: [Matplotlib-users] cycler v.0.10.0 released Message-ID: Folks, I am happy to announce the next release of Cycler. This will become the minimal version for the upcoming mpl v2.0 release. http://matplotlib.org/cycler/ Feature release for `cycler`. This release includes a number of new features: - `Cycler` objecst learned to generate an `itertools.cycle` by calling them, a-la a generator. - `Cycler` objects learned to change the name of a key via the new `.change_key(old_key, new_key)` method. - `Cycler` objects learned how to compare each other and determine if they are equal or not (`==`). - `Cycler` objects learned how to join another `Cycler` to be concatenated into a singel longer `Cycler` via `concat` method of function. `A.concat(B)` or `concat(A, B)`. - The `cycler` factory function learned to construct a complex `Cycler` from iterables provided as keyword arguments. - `Cycler` objects learn do show their insides with the `by_key` method which returns a dictionary of lists (instead of an iterable of dictionaries). Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncan.macleod at ligo.org Tue Feb 16 13:54:07 2016 From: duncan.macleod at ligo.org (Duncan Macleod) Date: Tue, 16 Feb 2016 12:54:07 -0600 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Hi all, I'm a member of the LIGO Scientific Collaboration, and an author on the PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of the graphs in this paper (not the detector layout). The paper is 'open-access' with a Creative Commons Attribution 3.0 License attached, so I believe the figures can be freely included in other documents as long as credits are given to the authors and the journal with an appropriate citation. It would be very nice to see this included as an example of using matplotlib for scientific analysis. Thanks D On 14 February 2016 at 07:52, Nils Becker wrote: > Hello everyone, > > as the direct observation of gravitational waves made its way round the > world a few days ago, I was pleased to see that they (very probably) used > matplotlib for their plots. They even used the new viridis colormap [1]. > I could not confirm this directly for the plots in the paper but at least > the data analysis stack at LIGO seems to be built partly on python. They > provide scripts to reproduce the data analysis in python and use matplotlib > to plot it [2]. > > In any case, maybe it's an idea to contact LIGO to confirm this and ask > them if we could put the figure on the website gallery as a kind of "plot > of honor" or something? I mean there is a chance that it's going to be the > most famous plot done in matplotlib to this date. > > Cheers > Nils > > [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 > (page 2) > [2] https://losc.ligo.org/software/ > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -- Duncan Macleod duncan.macleod at ligo.org LIGO Data Grid systems development Louisiana State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ben.v.root at gmail.com Tue Feb 16 14:00:34 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Tue, 16 Feb 2016 14:00:34 -0500 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Speaking of citations, while we have your ear... Some of us have noticed that the paper did not include any citations to the scientific software that were utilized. This is somewhat of a new thing to cite software, but matplotlib, numpy and other projects all have suggested citations that we encourage researchers to use in their papers. Many of us are also researchers, and contributions to projects like numpy and matplotlib are often not treated as being on the same level as any other publication because researchers rarely cite the software projects they use. http://matplotlib.org/citing.html No hard feelings, we love what you guys have done. Just flagging it so that you guys might do so in future papers. Cheers! Ben Root On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod wrote: > Hi all, > > I'm a member of the LIGO Scientific Collaboration, and an author on the > PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of > the graphs in this paper (not the detector layout). > > The paper is 'open-access' with a Creative Commons Attribution 3.0 License > attached, so I believe the figures can be freely included in other > documents as long as credits are given to the authors and the journal with > an appropriate citation. It would be very nice to see this included as an > example of using matplotlib for scientific analysis. > > > Thanks > D > > On 14 February 2016 at 07:52, Nils Becker wrote: > >> Hello everyone, >> >> as the direct observation of gravitational waves made its way round the >> world a few days ago, I was pleased to see that they (very probably) used >> matplotlib for their plots. They even used the new viridis colormap [1]. >> I could not confirm this directly for the plots in the paper but at least >> the data analysis stack at LIGO seems to be built partly on python. They >> provide scripts to reproduce the data analysis in python and use matplotlib >> to plot it [2]. >> >> In any case, maybe it's an idea to contact LIGO to confirm this and ask >> them if we could put the figure on the website gallery as a kind of "plot >> of honor" or something? I mean there is a chance that it's going to be the >> most famous plot done in matplotlib to this date. >> >> Cheers >> Nils >> >> [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 >> (page 2) >> [2] https://losc.ligo.org/software/ >> >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users at python.org >> https://mail.python.org/mailman/listinfo/matplotlib-users >> >> > > > -- > Duncan Macleod > duncan.macleod at ligo.org > LIGO Data Grid systems development > Louisiana State University > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncan.macleod at ligo.org Tue Feb 16 15:02:16 2016 From: duncan.macleod at ligo.org (Duncan Macleod) Date: Tue, 16 Feb 2016 14:02:16 -0600 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Hi Ben, all, You are correct, we haven't been very diligent in citing the software used in our results, mainly from the problem of having a very large software stack; everything from real-time interferometer operations and low-latency data analysis through detection characterisation and myriad offline analysis pipelines use hundreds of packages (C, C++, python, matlab, ROOT, ... on multiple OSs) which becomes hard to cite. I will, however, bring the subject up in the collaboration to try and collect citations from software so that we can get in the habit of providing proper references. Thanks for bringing this to our attention. Duncan On 16 February 2016 at 13:00, Benjamin Root wrote: > Speaking of citations, while we have your ear... > > Some of us have noticed that the paper did not include any citations to > the scientific software that were utilized. This is somewhat of a new thing > to cite software, but matplotlib, numpy and other projects all have > suggested citations that we encourage researchers to use in their papers. > Many of us are also researchers, and contributions to projects like numpy > and matplotlib are often not treated as being on the same level as any > other publication because researchers rarely cite the software projects > they use. > > http://matplotlib.org/citing.html > > No hard feelings, we love what you guys have done. Just flagging it so > that you guys might do so in future papers. > > Cheers! > Ben Root > > On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod > wrote: > >> Hi all, >> >> I'm a member of the LIGO Scientific Collaboration, and an author on the >> PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of >> the graphs in this paper (not the detector layout). >> >> The paper is 'open-access' with a Creative Commons Attribution 3.0 >> License attached, so I believe the figures can be freely included in other >> documents as long as credits are given to the authors and the journal with >> an appropriate citation. It would be very nice to see this included as an >> example of using matplotlib for scientific analysis. >> >> >> Thanks >> D >> >> On 14 February 2016 at 07:52, Nils Becker wrote: >> >>> Hello everyone, >>> >>> as the direct observation of gravitational waves made its way round the >>> world a few days ago, I was pleased to see that they (very probably) used >>> matplotlib for their plots. They even used the new viridis colormap [1]. >>> I could not confirm this directly for the plots in the paper but at >>> least the data analysis stack at LIGO seems to be built partly on python. >>> They provide scripts to reproduce the data analysis in python and use >>> matplotlib to plot it [2]. >>> >>> In any case, maybe it's an idea to contact LIGO to confirm this and ask >>> them if we could put the figure on the website gallery as a kind of "plot >>> of honor" or something? I mean there is a chance that it's going to be the >>> most famous plot done in matplotlib to this date. >>> >>> Cheers >>> Nils >>> >>> [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 >>> (page 2) >>> [2] https://losc.ligo.org/software/ >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users at python.org >>> https://mail.python.org/mailman/listinfo/matplotlib-users >>> >>> >> >> >> -- >> Duncan Macleod >> duncan.macleod at ligo.org >> LIGO Data Grid systems development >> Louisiana State University >> >> _______________________________________________ >> Matplotlib-users mailing list >> Matplotlib-users at python.org >> https://mail.python.org/mailman/listinfo/matplotlib-users >> >> > -- Duncan Macleod duncan.macleod at ligo.org LIGO Data Grid systems development Louisiana State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From ben.v.root at gmail.com Tue Feb 16 15:30:32 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Tue, 16 Feb 2016 15:30:32 -0500 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Duncan, You do bring up a very good point. With large projects like yours, it does become difficult to explicitly cite every single piece of software that was used, and how far does that go? For example, do you cite BLAS/ATLAS if you were using numpy? A citation for Linux? For gcc? Probably the best way to deal with that is to treat it like a dependency problem. When a paper is published, cite the software that was immediately used for the paper and/or any papers that have already been put out for a particular portion of the software stack. So, ideally, several LIGO papers would have already been put out about particular portions of the technical stack that goes into great detail, and would have cited software more exhaustively there. Then, this particular paper would only need to cite those kinds of papers rather than redoing the entire citation stack again and again. The software packages get their impact factor, and the authors and reader maintain their sanity. Yes, this is a bit of a chicken-n-egg problem because many editors frown upon "software papers". I personally had a paper rejected once partly because the editor thought I was shirking my authorship duties of describing the procedures by footnoting a github link and citing NumPy/SciPy and such. I am hopeful that these attitudes are changing, even in the past few years since I submitted that paper. Your team's work is in a fantastic position to broadly change these attitudes due to your visibility across the sciences. Already, your efforts to make the source code and data easily accessible has stunned many scientists who are not used to this level of openness. I work in an atmospheric research shop, and long-time researchers are just amazed by how easy it was to "run the simulation" themselves via the jupyter notebooks! Being atmospheric scientists, they never thought that they could possibly study anything astrophysics related with just a click of a link. Rock on! Ben Root On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod wrote: > Hi Ben, all, > > You are correct, we haven't been very diligent in citing the software used > in our results, mainly from the problem of having a very large software > stack; everything from real-time interferometer operations and low-latency > data analysis through detection characterisation and myriad offline > analysis pipelines use hundreds of packages (C, C++, python, matlab, ROOT, > ... on multiple OSs) which becomes hard to cite. > > I will, however, bring the subject up in the collaboration to try and > collect citations from software so that we can get in the habit of > providing proper references. Thanks for bringing this to our attention. > > > Duncan > > On 16 February 2016 at 13:00, Benjamin Root wrote: > >> Speaking of citations, while we have your ear... >> >> Some of us have noticed that the paper did not include any citations to >> the scientific software that were utilized. This is somewhat of a new thing >> to cite software, but matplotlib, numpy and other projects all have >> suggested citations that we encourage researchers to use in their papers. >> Many of us are also researchers, and contributions to projects like numpy >> and matplotlib are often not treated as being on the same level as any >> other publication because researchers rarely cite the software projects >> they use. >> >> http://matplotlib.org/citing.html >> >> No hard feelings, we love what you guys have done. Just flagging it so >> that you guys might do so in future papers. >> >> Cheers! >> Ben Root >> >> On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod >> wrote: >> >>> Hi all, >>> >>> I'm a member of the LIGO Scientific Collaboration, and an author on the >>> PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of >>> the graphs in this paper (not the detector layout). >>> >>> The paper is 'open-access' with a Creative Commons Attribution 3.0 >>> License attached, so I believe the figures can be freely included in other >>> documents as long as credits are given to the authors and the journal with >>> an appropriate citation. It would be very nice to see this included as an >>> example of using matplotlib for scientific analysis. >>> >>> >>> Thanks >>> D >>> >>> On 14 February 2016 at 07:52, Nils Becker >>> wrote: >>> >>>> Hello everyone, >>>> >>>> as the direct observation of gravitational waves made its way round the >>>> world a few days ago, I was pleased to see that they (very probably) used >>>> matplotlib for their plots. They even used the new viridis colormap [1]. >>>> I could not confirm this directly for the plots in the paper but at >>>> least the data analysis stack at LIGO seems to be built partly on python. >>>> They provide scripts to reproduce the data analysis in python and use >>>> matplotlib to plot it [2]. >>>> >>>> In any case, maybe it's an idea to contact LIGO to confirm this and ask >>>> them if we could put the figure on the website gallery as a kind of "plot >>>> of honor" or something? I mean there is a chance that it's going to be the >>>> most famous plot done in matplotlib to this date. >>>> >>>> Cheers >>>> Nils >>>> >>>> [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 >>>> (page 2) >>>> [2] https://losc.ligo.org/software/ >>>> >>>> _______________________________________________ >>>> Matplotlib-users mailing list >>>> Matplotlib-users at python.org >>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>> >>>> >>> >>> >>> -- >>> Duncan Macleod >>> duncan.macleod at ligo.org >>> LIGO Data Grid systems development >>> Louisiana State University >>> >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users at python.org >>> https://mail.python.org/mailman/listinfo/matplotlib-users >>> >>> >> > > > -- > Duncan Macleod > duncan.macleod at ligo.org > LIGO Data Grid systems development > Louisiana State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncan.macleod at ligo.org Tue Feb 16 15:59:39 2016 From: duncan.macleod at ligo.org (Duncan Macleod) Date: Tue, 16 Feb 2016 14:59:39 -0600 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Hi Ben, Thanks for your input, I hope we can get quickly to the point where papers with a smaller scope can cite the top-level software that enabled their research (for methods papers, etc), but it might take a bit longer to get the same for the full collaboration papers that have huge stacks underneath. Thanks D On 16 February 2016 at 14:30, Benjamin Root wrote: > Duncan, > > You do bring up a very good point. With large projects like yours, it does > become difficult to explicitly cite every single piece of software that was > used, and how far does that go? For example, do you cite BLAS/ATLAS if you > were using numpy? A citation for Linux? For gcc? > > Probably the best way to deal with that is to treat it like a dependency > problem. When a paper is published, cite the software that was immediately > used for the paper and/or any papers that have already been put out for a > particular portion of the software stack. So, ideally, several LIGO papers > would have already been put out about particular portions of the technical > stack that goes into great detail, and would have cited software more > exhaustively there. Then, this particular paper would only need to cite > those kinds of papers rather than redoing the entire citation stack again > and again. The software packages get their impact factor, and the authors > and reader maintain their sanity. > > Yes, this is a bit of a chicken-n-egg problem because many editors frown > upon "software papers". I personally had a paper rejected once partly > because the editor thought I was shirking my authorship duties of > describing the procedures by footnoting a github link and citing > NumPy/SciPy and such. I am hopeful that these attitudes are changing, even > in the past few years since I submitted that paper. Your team's work is in > a fantastic position to broadly change these attitudes due to your > visibility across the sciences. Already, your efforts to make the source > code and data easily accessible has stunned many scientists who are not > used to this level of openness. I work in an atmospheric research shop, and > long-time researchers are just amazed by how easy it was to "run the > simulation" themselves via the jupyter notebooks! Being atmospheric > scientists, they never thought that they could possibly study anything > astrophysics related with just a click of a link. > > Rock on! > > Ben Root > > > On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod > wrote: > >> Hi Ben, all, >> >> You are correct, we haven't been very diligent in citing the software >> used in our results, mainly from the problem of having a very large >> software stack; everything from real-time interferometer operations and >> low-latency data analysis through detection characterisation and myriad >> offline analysis pipelines use hundreds of packages (C, C++, python, >> matlab, ROOT, ... on multiple OSs) which becomes hard to cite. >> >> I will, however, bring the subject up in the collaboration to try and >> collect citations from software so that we can get in the habit of >> providing proper references. Thanks for bringing this to our attention. >> >> >> Duncan >> >> On 16 February 2016 at 13:00, Benjamin Root wrote: >> >>> Speaking of citations, while we have your ear... >>> >>> Some of us have noticed that the paper did not include any citations to >>> the scientific software that were utilized. This is somewhat of a new thing >>> to cite software, but matplotlib, numpy and other projects all have >>> suggested citations that we encourage researchers to use in their papers. >>> Many of us are also researchers, and contributions to projects like numpy >>> and matplotlib are often not treated as being on the same level as any >>> other publication because researchers rarely cite the software projects >>> they use. >>> >>> http://matplotlib.org/citing.html >>> >>> No hard feelings, we love what you guys have done. Just flagging it so >>> that you guys might do so in future papers. >>> >>> Cheers! >>> Ben Root >>> >>> On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod >> > wrote: >>> >>>> Hi all, >>>> >>>> I'm a member of the LIGO Scientific Collaboration, and an author on the >>>> PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of >>>> the graphs in this paper (not the detector layout). >>>> >>>> The paper is 'open-access' with a Creative Commons Attribution 3.0 >>>> License attached, so I believe the figures can be freely included in other >>>> documents as long as credits are given to the authors and the journal with >>>> an appropriate citation. It would be very nice to see this included as an >>>> example of using matplotlib for scientific analysis. >>>> >>>> >>>> Thanks >>>> D >>>> >>>> On 14 February 2016 at 07:52, Nils Becker >>>> wrote: >>>> >>>>> Hello everyone, >>>>> >>>>> as the direct observation of gravitational waves made its way round >>>>> the world a few days ago, I was pleased to see that they (very probably) >>>>> used matplotlib for their plots. They even used the new viridis colormap >>>>> [1]. >>>>> I could not confirm this directly for the plots in the paper but at >>>>> least the data analysis stack at LIGO seems to be built partly on python. >>>>> They provide scripts to reproduce the data analysis in python and use >>>>> matplotlib to plot it [2]. >>>>> >>>>> In any case, maybe it's an idea to contact LIGO to confirm this and >>>>> ask them if we could put the figure on the website gallery as a kind of >>>>> "plot of honor" or something? I mean there is a chance that it's going to >>>>> be the most famous plot done in matplotlib to this date. >>>>> >>>>> Cheers >>>>> Nils >>>>> >>>>> [1] >>>>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 >>>>> (page 2) >>>>> [2] https://losc.ligo.org/software/ >>>>> >>>>> _______________________________________________ >>>>> Matplotlib-users mailing list >>>>> Matplotlib-users at python.org >>>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>>> >>>>> >>>> >>>> >>>> -- >>>> Duncan Macleod >>>> duncan.macleod at ligo.org >>>> LIGO Data Grid systems development >>>> Louisiana State University >>>> >>>> _______________________________________________ >>>> Matplotlib-users mailing list >>>> Matplotlib-users at python.org >>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>> >>>> >>> >> >> >> -- >> Duncan Macleod >> duncan.macleod at ligo.org >> LIGO Data Grid systems development >> Louisiana State University >> > > -- Duncan Macleod duncan.macleod at ligo.org LIGO Data Grid systems development Louisiana State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From jklymak at uvic.ca Tue Feb 16 16:26:12 2016 From: jklymak at uvic.ca (Jody Klymak) Date: Tue, 16 Feb 2016 13:26:12 -0800 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: Hi Ben, > On 16 Feb 2016, at 12:30 PM, Benjamin Root wrote: > > Duncan, > > You do bring up a very good point. With large projects like yours, it does become difficult to explicitly cite every single piece of software that was used, and how far does that go? For example, do you cite BLAS/ATLAS if you were using numpy? A citation for Linux? For gcc? OK, so I have a data paper, where does a citation go? the software stack is *rarely* cited at all, unless the software author has made available a paper that uses a specialized technique that a reader would have trouble finding themselves. i.e. "the data was filtered with the Smith filter [Smith ?89]". There is rarely a statement in a paper that says ?Figure X was plotted with Matlab?, ?Figure y was plotted with GMT? and "Figure z was plotted with matplotlib?. Suggestions welcome - I value matplotlib, and don?t want to take advantage, but the request is a bit awkward to fulfill. Cheers, Jody > Rock on! > > Ben Root > > > On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod > wrote: > Hi Ben, all, > > You are correct, we haven't been very diligent in citing the software used in our results, mainly from the problem of having a very large software stack; everything from real-time interferometer operations and low-latency data analysis through detection characterisation and myriad offline analysis pipelines use hundreds of packages (C, C++, python, matlab, ROOT, ... on multiple OSs) which becomes hard to cite. > > I will, however, bring the subject up in the collaboration to try and collect citations from software so that we can get in the habit of providing proper references. Thanks for bringing this to our attention. > > > Duncan > > On 16 February 2016 at 13:00, Benjamin Root > wrote: > Speaking of citations, while we have your ear... > > Some of us have noticed that the paper did not include any citations to the scientific software that were utilized. This is somewhat of a new thing to cite software, but matplotlib, numpy and other projects all have suggested citations that we encourage researchers to use in their papers. Many of us are also researchers, and contributions to projects like numpy and matplotlib are often not treated as being on the same level as any other publication because researchers rarely cite the software projects they use. > > http://matplotlib.org/citing.html > > No hard feelings, we love what you guys have done. Just flagging it so that you guys might do so in future papers. > > Cheers! > Ben Root > > On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod > wrote: > Hi all, > > I'm a member of the LIGO Scientific Collaboration, and an author on the PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of the graphs in this paper (not the detector layout). > > The paper is 'open-access' with a Creative Commons Attribution 3.0 License attached, so I believe the figures can be freely included in other documents as long as credits are given to the authors and the journal with an appropriate citation. It would be very nice to see this included as an example of using matplotlib for scientific analysis. > > > Thanks > D > > On 14 February 2016 at 07:52, Nils Becker > wrote: > Hello everyone, > > as the direct observation of gravitational waves made its way round the world a few days ago, I was pleased to see that they (very probably) used matplotlib for their plots. They even used the new viridis colormap [1]. > I could not confirm this directly for the plots in the paper but at least the data analysis stack at LIGO seems to be built partly on python. They provide scripts to reproduce the data analysis in python and use matplotlib to plot it [2]. > > In any case, maybe it's an idea to contact LIGO to confirm this and ask them if we could put the figure on the website gallery as a kind of "plot of honor" or something? I mean there is a chance that it's going to be the most famous plot done in matplotlib to this date. > > Cheers > Nils > > [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 (page 2) > [2] https://losc.ligo.org/software/ > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > > > > -- > Duncan Macleod > duncan.macleod at ligo.org > LIGO Data Grid systems development > Louisiana State University > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > > > > > -- > Duncan Macleod > duncan.macleod at ligo.org > LIGO Data Grid systems development > Louisiana State University > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users -- Jody Klymak http://web.uvic.ca/~jklymak/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ben.v.root at gmail.com Tue Feb 16 16:47:41 2016 From: ben.v.root at gmail.com (Benjamin Root) Date: Tue, 16 Feb 2016 16:47:41 -0500 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: In latex, you could utilize the \nocite{} feature. I've done this on certain occasions. *Including references that are not cited in the paper.* Bibtex builds the bibliography from the references that are actually cited in the paper. Including references without corresponding citations is generally a bad idea, but it may be warranted in special situations. To include a reference that is not cited in the paper, but which has a record in the bibtex database, add the command \nocite{xxx} at the end of the paper, just before the bibliography; here "xxx" is the key for the paper to be cited. The command \nocite{*} causes all items in the database to be included in the references, regardless of whether or not they are cited in the paper. http://www.math.uiuc.edu/~hildebr/tex/bibliographies0.html On Tue, Feb 16, 2016 at 4:26 PM, Jody Klymak wrote: > > Hi Ben, > > On 16 Feb 2016, at 12:30 PM, Benjamin Root wrote: > > Duncan, > > You do bring up a very good point. With large projects like yours, it does > become difficult to explicitly cite every single piece of software that was > used, and how far does that go? For example, do you cite BLAS/ATLAS if you > were using numpy? A citation for Linux? For gcc? > > > OK, so I have a data paper, where does a citation go? the software stack > is *rarely* cited at all, unless the software author has made available a > paper that uses a specialized technique that a reader would have trouble > finding themselves. i.e. "the data was filtered with the Smith filter > [Smith ?89]". > > There is rarely a statement in a paper that says ?Figure X was plotted > with Matlab?, ?Figure y was plotted with GMT? and "Figure z was plotted > with matplotlib?. > > Suggestions welcome - I value matplotlib, and don?t want to take > advantage, but the request is a bit awkward to fulfill. > > Cheers, Jody > > > > Rock on! > > Ben Root > > > On Tue, Feb 16, 2016 at 3:02 PM, Duncan Macleod > wrote: > >> Hi Ben, all, >> >> You are correct, we haven't been very diligent in citing the software >> used in our results, mainly from the problem of having a very large >> software stack; everything from real-time interferometer operations and >> low-latency data analysis through detection characterisation and myriad >> offline analysis pipelines use hundreds of packages (C, C++, python, >> matlab, ROOT, ... on multiple OSs) which becomes hard to cite. >> >> I will, however, bring the subject up in the collaboration to try and >> collect citations from software so that we can get in the habit of >> providing proper references. Thanks for bringing this to our attention. >> >> >> Duncan >> >> On 16 February 2016 at 13:00, Benjamin Root wrote: >> >>> Speaking of citations, while we have your ear... >>> >>> Some of us have noticed that the paper did not include any citations to >>> the scientific software that were utilized. This is somewhat of a new thing >>> to cite software, but matplotlib, numpy and other projects all have >>> suggested citations that we encourage researchers to use in their papers. >>> Many of us are also researchers, and contributions to projects like numpy >>> and matplotlib are often not treated as being on the same level as any >>> other publication because researchers rarely cite the software projects >>> they use. >>> >>> http://matplotlib.org/citing.html >>> >>> No hard feelings, we love what you guys have done. Just flagging it so >>> that you guys might do so in future papers. >>> >>> Cheers! >>> Ben Root >>> >>> On Tue, Feb 16, 2016 at 1:54 PM, Duncan Macleod >> > wrote: >>> >>>> Hi all, >>>> >>>> I'm a member of the LIGO Scientific Collaboration, and an author on the >>>> PRL paper linked by Nils. Figure 1 did indeed use matplotlib, as did all of >>>> the graphs in this paper (not the detector layout). >>>> >>>> The paper is 'open-access' with a Creative Commons Attribution 3.0 >>>> License attached, so I believe the figures can be freely included in other >>>> documents as long as credits are given to the authors and the journal with >>>> an appropriate citation. It would be very nice to see this included as an >>>> example of using matplotlib for scientific analysis. >>>> >>>> >>>> Thanks >>>> D >>>> >>>> On 14 February 2016 at 07:52, Nils Becker >>>> wrote: >>>> >>>>> Hello everyone, >>>>> >>>>> as the direct observation of gravitational waves made its way round >>>>> the world a few days ago, I was pleased to see that they (very probably) >>>>> used matplotlib for their plots. They even used the new viridis colormap >>>>> [1]. >>>>> I could not confirm this directly for the plots in the paper but at >>>>> least the data analysis stack at LIGO seems to be built partly on python. >>>>> They provide scripts to reproduce the data analysis in python and use >>>>> matplotlib to plot it [2]. >>>>> >>>>> In any case, maybe it's an idea to contact LIGO to confirm this and >>>>> ask them if we could put the figure on the website gallery as a kind of >>>>> "plot of honor" or something? I mean there is a chance that it's going to >>>>> be the most famous plot done in matplotlib to this date. >>>>> >>>>> Cheers >>>>> Nils >>>>> >>>>> [1] >>>>> http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.061102 >>>>> (page 2) >>>>> [2] https://losc.ligo.org/software/ >>>>> >>>>> _______________________________________________ >>>>> Matplotlib-users mailing list >>>>> Matplotlib-users at python.org >>>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>>> >>>>> >>>> >>>> >>>> -- >>>> Duncan Macleod >>>> duncan.macleod at ligo.org >>>> LIGO Data Grid systems development >>>> Louisiana State University >>>> >>>> _______________________________________________ >>>> Matplotlib-users mailing list >>>> Matplotlib-users at python.org >>>> https://mail.python.org/mailman/listinfo/matplotlib-users >>>> >>>> >>> >> >> >> -- >> Duncan Macleod >> duncan.macleod at ligo.org >> LIGO Data Grid systems development >> Louisiana State University >> > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > > -- > Jody Klymak > http://web.uvic.ca/~jklymak/ > > > > > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilja.j.honkonen at nasa.gov Tue Feb 16 16:42:14 2016 From: ilja.j.honkonen at nasa.gov (Ilja Honkonen) Date: Tue, 16 Feb 2016 16:42:14 -0500 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: <56C397B6.1000707@nasa.gov> Hi > OK, so I have a data paper, where does a citation go? the software > stack is *rarely* cited at all, unless the software author has made > available a paper that uses a specialized technique that a reader would > have trouble finding themselves. i.e. "the data was filtered with the > Smith filter [Smith ?89]". > > There is rarely a statement in a paper that says ?Figure X was plotted > with Matlab?, ?Figure y was plotted with GMT? and "Figure z was plotted > with matplotlib?. > > Suggestions welcome - I value matplotlib, and don?t want to take > advantage, but the request is a bit awkward to fulfill. How about acknowledgements section? Perhaps listing how each figure was made is too verbose but maybe something like: I/we thank the contributors of matplotlib [ref N] for making the software freely available. Ilja From efiring at hawaii.edu Tue Feb 16 16:52:30 2016 From: efiring at hawaii.edu (Eric Firing) Date: Tue, 16 Feb 2016 11:52:30 -1000 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: <56C39A1E.5060603@hawaii.edu> On 2016/02/16 11:47 AM, Benjamin Root wrote: > Including references without corresponding citations is generally a bad > idea, but it may be warranted in special situations. I think that if they are paying attention, the copy editors for our journals would strip those out. Eric From jklymak at uvic.ca Tue Feb 16 16:57:36 2016 From: jklymak at uvic.ca (Jody Klymak) Date: Tue, 16 Feb 2016 13:57:36 -0800 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: > On 16 Feb 2016, at 13:47 PM, Benjamin Root wrote: > > In latex, you could utilize the \nocite{} feature. I've done this on certain occasions. > > Including references that are not cited in the paper. Bibtex builds the bibliography from the references that are actually cited in the paper. Including references without corresponding citations is generally a bad idea, but it may be warranted in special situations. To include a reference that is not cited in the paper, but which has a record in the bibtex database, add the command \nocite{xxx} at the end of the paper, just before the bibliography; here "xxx" is the key for the paper to be cited. The command \nocite{*} causes all items in the database to be included in the references, regardless of whether or not they are cited in the paper. Most journals I?m familiar with will not let you put uncited references into the reference section, for sadly obvious reasons ;-) The acknowledgements section is fine, the only issue being where does one draw the line? I guess in the methods section simply saying, plots were rendered using matplotlib \cite{hunter} isn?t a terrible solution. Not usually done, but if it helps matplotlib stay funded, then its probably worth it. Apologies in advance for my recent paper where I didn?t do this, but its probably less well publicized than the LIGO paper, so maybe I?ll get away w/ it. Cheers, Jody -- Jody Klymak http://web.uvic.ca/~jklymak/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From kathleen.m.tacina at nasa.gov Tue Feb 16 17:53:53 2016 From: kathleen.m.tacina at nasa.gov (Kathleen Tacina) Date: Tue, 16 Feb 2016 17:53:53 -0500 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: References: Message-ID: <56C3A881.2030209@nasa.gov> I've occasionally put software like matplotlib in the Acknowledgements section, and included a reference there. I wasn't aware of \nocite, I may use it in the future. On 2/16/16 4:48 PM, matplotlib-users-request at python.org wrote: > Re: matplotlib at LIGO/GW observation From julien.hillairet at gmail.com Wed Feb 17 02:14:10 2016 From: julien.hillairet at gmail.com (Julien Hillairet) Date: Wed, 17 Feb 2016 08:14:10 +0100 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: <56C3A881.2030209@nasa.gov> References: <56C3A881.2030209@nasa.gov> Message-ID: I think a default addition in the Acknowledgements, with a citation, (because it's important for automatic scholar tools, like G.Scholar or H-factor calculations...) would probably be the best combination. Indeed, something like : "The author(s) thank the contributors of Matplotlib [Hunter:2007] for making the software freely available." 2016-02-16 23:53 GMT+01:00 Kathleen Tacina : > I've occasionally put software like matplotlib in the Acknowledgements > section, and included a reference there. > > I wasn't aware of \nocite, I may use it in the future. > > On 2/16/16 4:48 PM, matplotlib-users-request at python.org wrote: > >> Re: matplotlib at LIGO/GW observation >> > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gustavo.goretkin at gmail.com Fri Feb 26 15:12:58 2016 From: gustavo.goretkin at gmail.com (Gustavo Goretkin) Date: Fri, 26 Feb 2016 15:12:58 -0500 Subject: [Matplotlib-users] rotated axes within figure. Message-ID: Hello, (sorry if you get this message twice. I originally posted to the old sourceforge list) How can I add an axes to a figure, but specify the transform from axes coordinates to figure coordinates? I want a set of axes (ticks, spines, data, everything) that are rotated? Figure.add_axes [1] accepts a box left-bottom-width-height axis aligned box specification. I can't follow in the code where a transform is made out of that, but I basically want a generic transform. Do tick labels, ticks, titles, etc. assume that the axes-to-figure transform is purely a translation? [1] https://github.com/matplotlib/matplotlib/blob/e12d103a11cd08adbed348547bdb8182e414e0bb/lib/matplotlib/figure.py#L840 Thanks, Gustavo -------------- next part -------------- An HTML attachment was scrubbed... URL: From gustavo.goretkin at gmail.com Mon Feb 29 03:39:47 2016 From: gustavo.goretkin at gmail.com (Gustavo Goretkin) Date: Mon, 29 Feb 2016 03:39:47 -0500 Subject: [Matplotlib-users] rotated axes within figure. In-Reply-To: References: Message-ID: Alright, this was my shot at it: https://gist.github.com/goretkin/d34f287062f6b27e8846 It seems like the assumption of an axis-aligned axes is baked in pretty strongly, and maybe that's for the best... I couldn't figure out how tick lines work and why they weren't rotated. The Line2D object has the correct transform. They are lines whose xy_data contain only one coordinate, though something must specify the other end of the tick line (what gives it its length otherwise?) and that is assuming that the axes is axis-aligned. In [4]: [l.get_xydata() for l in ax.xaxis.get_ticklines()] Out[4]: [array([[ 0., 0.]]), array([[ 0., 1.]]), array([[ 2., 0.]]), array([[ 2., 1.]]), array([[ 4., 0.]]), array([[ 4., 1.]]), array([[ 6., 0.]]), array([[ 6., 1.]]), array([[ 8., 0.]]), array([[ 8., 1.]]), array([[ 10., 0.]]), array([[ 10., 1.]]), array([[ 12., 0.]]), array([[ 12., 1.]])] On Fri, Feb 26, 2016 at 3:12 PM, Gustavo Goretkin < gustavo.goretkin at gmail.com> wrote: > Hello, > > (sorry if you get this message twice. I originally posted to the old > sourceforge list) > > How can I add an axes to a figure, but specify the transform from axes > coordinates to figure coordinates? I want a set of axes (ticks, spines, > data, everything) that are rotated? > > Figure.add_axes [1] accepts a box left-bottom-width-height axis aligned > box specification. I can't follow in the code where a transform is made out > of that, but I basically want a generic transform. Do tick labels, ticks, > titles, etc. assume that the axes-to-figure transform is purely a > translation? > > > [1] > https://github.com/matplotlib/matplotlib/blob/e12d103a11cd08adbed348547bdb8182e414e0bb/lib/matplotlib/figure.py#L840 > > Thanks, > Gustavo > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joferkington at gmail.com Mon Feb 29 07:16:11 2016 From: joferkington at gmail.com (Joe Kington) Date: Mon, 29 Feb 2016 06:16:11 -0600 Subject: [Matplotlib-users] rotated axes within figure. In-Reply-To: References: Message-ID: For what it's worth, if you don't mind having fixed extents, you can use axisartist for this. There's an example of it in the axisartist examples and a simplified version here: http://stackoverflow.com/a/21654433/325565 Hope that helps! -Joe On Feb 29, 2016 2:42 AM, "Gustavo Goretkin" wrote: > Alright, this was my shot at it: > https://gist.github.com/goretkin/d34f287062f6b27e8846 > > It seems like the assumption of an axis-aligned axes is baked in pretty > strongly, and maybe that's for the best... > > I couldn't figure out how tick lines work and why they weren't rotated. > The Line2D object has the correct transform. They are lines whose xy_data > contain only one coordinate, though something must specify the other end of > the tick line (what gives it its length otherwise?) and that is assuming > that the axes is axis-aligned. > > > In [4]: [l.get_xydata() for l in ax.xaxis.get_ticklines()] > Out[4]: > [array([[ 0., 0.]]), > array([[ 0., 1.]]), > array([[ 2., 0.]]), > array([[ 2., 1.]]), > array([[ 4., 0.]]), > array([[ 4., 1.]]), > array([[ 6., 0.]]), > array([[ 6., 1.]]), > array([[ 8., 0.]]), > array([[ 8., 1.]]), > array([[ 10., 0.]]), > array([[ 10., 1.]]), > array([[ 12., 0.]]), > array([[ 12., 1.]])] > > > > On Fri, Feb 26, 2016 at 3:12 PM, Gustavo Goretkin < > gustavo.goretkin at gmail.com> wrote: > >> Hello, >> >> (sorry if you get this message twice. I originally posted to the old >> sourceforge list) >> >> How can I add an axes to a figure, but specify the transform from axes >> coordinates to figure coordinates? I want a set of axes (ticks, spines, >> data, everything) that are rotated? >> >> Figure.add_axes [1] accepts a box left-bottom-width-height axis aligned >> box specification. I can't follow in the code where a transform is made out >> of that, but I basically want a generic transform. Do tick labels, ticks, >> titles, etc. assume that the axes-to-figure transform is purely a >> translation? >> >> >> [1] >> https://github.com/matplotlib/matplotlib/blob/e12d103a11cd08adbed348547bdb8182e414e0bb/lib/matplotlib/figure.py#L840 >> >> Thanks, >> Gustavo >> > > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilja.j.honkonen at nasa.gov Tue Feb 9 09:59:05 2016 From: ilja.j.honkonen at nasa.gov (Ilja Honkonen) Date: Tue, 09 Feb 2016 14:59:05 -0000 Subject: [Matplotlib-users] How to plot tick values in-place Message-ID: <56B9FD1F.1010609@nasa.gov> Hello I haven't been able to find a solution to this problem with google, perhaps someone here can help. When I plot the following: import matplotlib.pyplot as plot plot.plot([0, 1e-9, 0, -1e-9]) plot.show() the y tick marks are shown as -1, -0.5, 0, 0.5, 1 and their scaling is given elsewhere, how can I make matplotlib write the entire number at tick location so I don't have to search for potential corrections to tick values in other parts of the plot? matplotlib.__version__ is '1.1.1'. Thanks! Ilja From sundar_ima at rediffmail.com Thu Feb 11 13:36:39 2016 From: sundar_ima at rediffmail.com (sundar_ima) Date: Thu, 11 Feb 2016 18:36:39 -0000 Subject: [Matplotlib-users] What is the fastest way to plot map using Basemap and shapefile? Message-ID: <1455215798101-46743.post@n5.nabble.com> As the title suggest What is the fastest way to plot map using Basemap and python? I have a requirement of plotting 100s of images for a area where basemap does not have the better resolution. Therefore I have choose to plot shapefile for boundary and basemap for projection. I have already read this file https://github.com/matplotlib/basemap/blob/master/examples/hires.py and it seems to be the way ahead for plotting maps faster. However, when I tried to do the same example for shapefile, the current axis gets removed. Here is my work flow:- import required modeules # initialise basemap m = Basemap(projection='merc', llcrnrlat=south, urcrnrlat=north, llcrnrlon=west, urcrnrlon=east, resolution='c', area_thresh=10000.) # I have a seperate plotting function def drawmap(data, string1, strin2, strin3): print 'Plotting the actual map.' F = plt.gcf() # Gets the current figure for later use ..... do some code def plot_variable(): .... some code # call the drawmap function drawmap(data, string1, strin2, strin3) plot_variable() If I use the following line just after Basemap instance all works fine without any error (though that is what I want as the boundaries wont be plotted later). The same line included with the def drawmap(data, string1, strin2, strin3): function also works fine but increases the plot time as it has to read every time the drawmap function is called. m.readshapefile('data/gis-data/NaturalEarth_10M_India_corrected/world_countries/ne_10m_admin_0_countries_lakes', 'ne_10m_admin_0_countries_lakes', drawbounds=True, linewidth=0.7) Then I tried to pickle the above line from outside the drawmap(data, string1, strin2, strin3) function and reload it after whenever drawmap is called. However, I get the following error:- F.add_axes(cax) # Adds the new axis to the figure as the current working axis File "/home/sundar/anaconda2/lib/python2.7/site-packages/matplotlib/figure.py", line 901, in add_axes raise ValueError(msg) ValueError: The Axes must have been created in the present figure Any solution for above or any I dea to plot faster is appreciated. -- View this message in context: http://matplotlib.1069221.n5.nabble.com/What-is-the-fastest-way-to-plot-map-using-Basemap-and-shapefile-tp46743.html Sent from the matplotlib - users mailing list archive at Nabble.com. From StefanProbst at gmx.net Mon Feb 15 03:41:37 2016 From: StefanProbst at gmx.net (sprobst76) Date: Mon, 15 Feb 2016 08:41:37 -0000 Subject: [Matplotlib-users] Graph similiar to necked_tensile_specimen.png Message-ID: <1455524618872-46752.post@n5.nabble.com> Hello, in the examples I found a graph which is similar to a graph I want to have. However the example is only given as png and I want to have the code. The example is the necked_tensile_specimen.pngimage of the following example http://matplotlib.org/examples/images_contours_and_fields/interpolation_none_vs_nearest.html There is a 2D map which is compressed in the center. Does anybody has the code for the example? Thank you & best regards Stefan -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Graph-similiar-to-necked-tensile-specimen-png-tp46752.html Sent from the matplotlib - users mailing list archive at Nabble.com. From chinchi at physik.tu-berlin.de Mon Feb 15 05:03:51 2016 From: chinchi at physik.tu-berlin.de (superchinchilla) Date: Mon, 15 Feb 2016 10:03:51 -0000 Subject: [Matplotlib-users] Struggle with ticker.SymmetricalLogLocator() Message-ID: <1455530629905-46753.post@n5.nabble.com> Hi, I want to make a symmetric logarithmic plot, but unfortunately the y-values are overlapping around 0. I don't want to display the first values around 0. I'm not sure how to use the ticker.SymmetricalLogLocator command to change the ticklocations or the tickfrequencies. I searched for a long time but didn't find any proper solution for it besides the examples for the normal Loglocater which didn't work. I tried to understand how the ticker.SymmetricalLogLocator(transform, subs=None) instance is working on the matplotlib documentation side which is not an easy target for me. I only want that the first ticklabes around zero are not displayed in my plot. I'm using the plt.yscale('symlog') command in order to plot it symmetrically around zero. My picture looks like Sorry for my bad English, thanx for any help in advance -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Struggle-with-ticker-SymmetricalLogLocator-tp46753.html Sent from the matplotlib - users mailing list archive at Nabble.com. From npkuin at gmail.com Tue Feb 16 18:41:43 2016 From: npkuin at gmail.com (Paul Kuin) Date: Tue, 16 Feb 2016 23:41:43 -0000 Subject: [Matplotlib-users] matplotlib at LIGO/GW observation In-Reply-To: <56C3A881.2030209@nasa.gov> References: <56C3A881.2030209@nasa.gov> Message-ID: There is a certain unfairness in the citing when the citation goes to a review paper, not to the source. Similarly, for software when the problem is that not all the parts that contributed can be referenced, a software paper describing the software, processing and what bit are used from here and there will at least set up some traceability. On Tue, Feb 16, 2016 at 10:53 PM, Kathleen Tacina < kathleen.m.tacina at nasa.gov> wrote: > I've occasionally put software like matplotlib in the Acknowledgements > section, and included a reference there. > > I wasn't aware of \nocite, I may use it in the future. > > On 2/16/16 4:48 PM, matplotlib-users-request at python.org wrote: > >> Re: matplotlib at LIGO/GW observation >> > > _______________________________________________ > Matplotlib-users mailing list > Matplotlib-users at python.org > https://mail.python.org/mailman/listinfo/matplotlib-users > -- * * * * * * * * http://www.mssl.ucl.ac.uk/~npmk/ * * * * Dr. N.P.M. Kuin (n.kuin at ucl.ac.uk) phone +44-(0)1483 (prefix) -204211 (work) mobile +44(0)7806985366 skype ID: npkuin Mullard Space Science Laboratory ? University College London ? Holmbury St Mary ? Dorking ? Surrey RH5 6NT? U.K. -------------- next part -------------- An HTML attachment was scrubbed... URL: From msharmavikram at gmail.com Mon Feb 22 04:07:23 2016 From: msharmavikram at gmail.com (msharmvikram) Date: Mon, 22 Feb 2016 09:07:23 -0000 Subject: [Matplotlib-users] Installing matplotlib1.5.1 in python3.5 and linux Message-ID: <1456131012420-46786.post@n5.nabble.com> Hi I am trying to install matplotlib 1.5.0 /1.5.1 version in my CentOS7 -- Python3.5 active machine. I have resolved all the dependencies stated in the INSTALL file and also have updated setuptools to latest one. However, to my bad luck i am not able to resolve this one particular issue shown in the image. I have tried following ways of install 1) pip3 install matplotlib==1.5.1 2) easy_install-3.5 -m matplotlib Both results in same above issue. I am clueless on what is the problem. Anyone solved this issue? -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Installing-matplotlib1-5-1-in-python3-5-and-linux-tp46786.html Sent from the matplotlib - users mailing list archive at Nabble.com. From salonirao2 at gmail.com Mon Feb 22 09:54:40 2016 From: salonirao2 at gmail.com (Saloni Rao) Date: Mon, 22 Feb 2016 14:54:40 -0000 Subject: [Matplotlib-users] Curve Fitting Message-ID: <14431787-2565-4D06-BCC1-32DF719FEC00@gmail.com> Hi, I was trying to write some Ipython code for Non linear Model fitting for a complex formula( having polynomials in numerator and denominator). It has 3 variables for which data is available and 3 variable which have to be fitted. For data I have an excel file from which I am uploading the data. I tried using scipy.optimize, lmfit and kmpfit but failed badly. Could you suggest me a way to work around this problem? Thanks. From hamid1rajabi at gmail.com Fri Feb 26 05:49:49 2016 From: hamid1rajabi at gmail.com (hamid.rajabi) Date: Fri, 26 Feb 2016 03:49:49 -0700 (MST) Subject: [Matplotlib-users] Importing pylab Message-ID: <1456483789807-46800.post@n5.nabble.com> Dear all, I have installed matplotlib modul on python 2.7 and it works perfectly. just when I want to import "pylab" module, I receive this error: " Traceback (most recent call last): File "", line 1, in import pylab File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pylab.py", line 1, in File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/pylab.py", line 231, in import matplotlib.finance File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/finance.py", line 38, in from matplotlib.collections import LineCollection, PolyCollection File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/collections.py", line 27, in import matplotlib.backend_bases as backend_bases File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 56, in import matplotlib.textpath as textpath File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/textpath.py", line 19, in import matplotlib.font_manager as font_manager File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/font_manager.py", line 58, in from matplotlib import ft2font ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/ft2font.so, 2): Library not loaded: @loader_path/../../../libfreetype.6.dylib Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/ft2font.so Reason: image not found " Please Help me. -- View this message in context: http://matplotlib.1069221.n5.nabble.com/Importing-pylab-tp46800.html Sent from the matplotlib - users mailing list archive at Nabble.com.