Mailman 3 June 2018 - Matplotlib-users

Formatting numbers in "nicer" scientific notation
by Daniele Nicolodi June 30, 2018

June 30, 2018

Hello all, sorry for the vague title, but I didn't know how else to formulate it. I'm looking for a facility to format numbers in a nicer way, namely to turno 3.14e-5 into something like $3.14 \times 10^{\minus 5}$. I'm almost sure I've seen something like that in matplotlib somewhere but I'm not able to find it anymore. Is my recollection wrong? Does anyone know if that is implemented by some other library? Thank you. Cheers, Dan

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Bizarre clipping of title when markers used
by Neal Becker June 12, 2018

June 12, 2018

I haven't been able to reproduce yet in a minimal example, but in this code, if markers are used in the plot, then the title is clipped off and not shown. If the markers= is commented out, then the title is fine. I know it's clipped, because if I specify set_title ('blah', y=0.5) < set y to something < .95 Then the title is displayed (but in the wrong position). So, if markers are present, title is clipped off. No markers, title is fine. My code is here (you can't run it I'm afraid): matplotlib=2.2.2 import pandas as pd def do_plot(other_csv, mine_xlsx, name): df_tdla_96 = pd.read_csv (other_csv) df_tdla_96_mine = pd.read_excel (mine_xlsx) df_tdla_96_mine = df_tdla_96_mine[['esno_corrected', 'per']] df_tdla_96_mine.rename (index=str, columns={'esno_corrected' : 'SNR', 'per' : 'Hughes'}, inplace=True) df_tdla_96.drop(labels='Hughes', inplace=True, axis=1) df_tdla_96_merge = pd.merge(left=df_tdla_96, right=df_tdla_96_mine, on='SNR') from matplotlib.lines import Line2D from itertools import cycle m_cycle = cycle(Line2D.filled_markers) import matplotlib.pyplot as plt fig, ax = plt.subplots()#, sharex=True) for company in df_tdla_96_merge.columns[1:]: df = df_tdla_96_merge[['SNR', company]] ax.semilogy(df['SNR'], df[company], marker='x') ax.set_title('Simple plot') #ax.set_title('blah', fontsize=12, y=0.95) # ax.set_xlabel('SNR') # ax.set_ylabel('BLER') # ax.legend(loc='best') #fig.suptitle('blah', fontsize=12, x=0.5, y=0.9) ax.grid() #plt.tight_layout() plt.show() #plt.tight_layout() #plt.savefig('tdla_96.pdf') do_plot('tdla_96_other.csv', 'tdla_96_mrc_wiener.xlsx', 'TDLA 96 CP-OFDM')

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Re: [Matplotlib-users] specify line plot color
by vincent.adrien＠gmail.com June 10, 2018

June 10, 2018

Hi alberto, If I have correctly understood your wish, you may be looking for in [numpy.savetxt](https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/… and [numpy.loadtxt](https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/…. This may not be really Matplotlib's field anymore, but please find attached a small example on how to record data into a flat text file and reload them. Hopefully this will helpful to you. Best regards, Adrien On 06/10/2018 08:30 AM, alberto wrote: > Hi, > I wrote days ago about script python > I would ask you if exist a way to print in a file the data of a plot > > this is my script > > > #!/usr/bin/env python > > > import numpy as np > import matplotlib.pyplot as plt > import sys > > #%% > # Temperature that we are interested in > target_T = 10.0 > #%% Load all condtens data > data = np.loadtxt("Pb8I28-MA-BISIMID_101010Kp_FR.condtens") > #%% Load trace data > data2 = np.loadtxt("Pb8I28-MA-BISIMID_101010Kp_FR.trace") > #print(data[:,1]) > #%% > # Select only the data points computed at that specific temperature > T = data[:, 1] > indices = (T == target_T) > #print(indices) > > #%%Fermi levels converted in electronvolts > Ef = 13.60 * data[indices, 0] > print(Ef) > > > #%% plot trace at T > Fermi_level = 4.44075 # (in eV) > > plt.figure() > labels = ("$\sigma$ / $tau$",) > for i, label in enumerate(labels): > plt.plot((Ef - Fermi_level), data2[indices,(abs(5))], label=label) > plt.legend(loc="best") > plt.xlabel(r"Energy-Efermi [eV]") > plt.ylabel(r"$\sigma$/$\tau$ [$\Omega$ m s]") > plt.tight_layout() > plt.show() > > > #%% plot DOS(Ef) at T > > au_to_m = 5.291772083E-11 > V = 7670.7134 # a.u.^3 > m_el = 9.10938356E-31 #Kg > V_m3 = V*(au_to_m)**3 > print(V_m3) > > plt.figure() > labels = ("DOS",) > for i, label in enumerate(labels): > plt.plot(Ef, data2[indices,(3)], label=label) > plt.legend(loc="best") > plt.xlabel(r"Ef [eV]") > plt.ylabel(r"n /($\mu)$ [e / m^3]") > plt.tight_layout() > plt.show() > > > #%% > # And recast as an array of 3x3 matrices for convenience > # Column numbers are easy to follow: 1 for Ef, 1 for T, 1 for N, 9 for > sigma, > # and then comes the Seebeck coefficient > sigma = data[indices, 3:12].reshape((-1, 3, 3)) > sys.stdout=open('prova.txt','wt') > print(sigma) > seebeck = data[indices, 12:21].reshape((-1, 3, 3)) > > # Plot the xx, yy and zz components as a function of the first column > plt.figure() > labels = ("xx", "yy", "zz") > for i, label in enumerate(labels): > plt.plot(Ef, sigma[:, i, i], label=label) > plt.legend(loc="best") > plt.xlabel(r"Energy [eV]") > plt.ylabel(r"$\sigma$ [1/$\Omega$ m s]") > #plt.axis([4,8,-1,8]) > plt.tight_layout() > plt.show() > > > in particular I would write four columns with ef and xx yy zz in a > datafile.txt > > regards > > Alberto > > 2018-04-16 19:22 GMT+02:00 alberto <voodoo.bender(a)gmail.com > <mailto:voodoo.bender@gmail.com>>: > > Hi, > thank you so much for your help > > Alberto > > 2018-04-16 18:58 GMT+02:00 vincent.adrien(a)gmail.com > <mailto:vincent.adrien@gmail.com> <vincent.adrien(a)gmail.com > <mailto:vincent.adrien@gmail.com>>: > > Hi Alberto, > > I now understand better. No need to flip you data then: you can > actually explicitly specify the color that you want in the > `plot` function, with the *color* keyword argument. See the > attached script that should hopefully help you to get what you want. > > Best regards, > Adrien > > On 04/16/2018 09:20 AM, alberto wrote: > > Hi vincet, > > in my plot (see .png file) > > I would invert the color > > xx --> green > zz--> blue > > > > regards > > Alberto > > > Pb8I28-MA-PERF-BISIMID_32Kp_101010.condtens > <https://drive.google.com/file/d/17YnBjb-8IlL8e_0Kcxj_Y97cJr_adCi4/view?usp=… > <https://drive.google.com/file/d/17YnBjb-8IlL8e_0Kcxj_Y97cJr_adCi4/view?usp=…>> > > > > >

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HiLo colormap
by Juan Nunez-Iglesias June 10, 2018

June 10, 2018

Hi, Would a PR to add HiLo to Matplotlib be welcome? It seems very useful in general and especially in scientific data analysis, see e.g. https://postacquisition.wordpress.com/2015/08/25/go-west-ern/ See also this StackOverflow question: https://stackoverflow.com/questions/44116995/how-to-achieve-the-fiji-hilo-c… Juan.

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First Time asking a question
by Matthew Bradley June 8, 2018

June 8, 2018

Hi all, This is my first time asking a question on this channel so everyone's help is appreciated. I'm trying to recreate a figure that my research lab first created in mathematica (attached in the email). I've tried to recreate the figure and plot area using the gridspec feature, and it's come close (my closest attempt is also attached). There are still a few things that need tweaking like making the lower right plot a square shape, decreasing the spacing between it and the plot to the left and above it. Here's my code as a starting point if you wanted to use it. The figure size doesn't have to be 25:20. fig = plt.figure(figsize=(25,20)) gs1 = gridspec.GridSpec(7,10) ax1 = plt.subplot(gs1[1:,0]) ax2 = plt.subplot(gs1[0:6,1]) ax3 = plt.subplot(gs1[1:,3]) ax4 = plt.subplot(gs1[0:6,4]) ax5 = plt.subplot(gs1[1,6]) ax6 = plt.subplot(gs1[0,7]) ax7 = plt.subplot(gs1[0,9]) ax8 = plt.subplot(gs1[4:,6:]) gs1.update(wspace=0.02,hspace=0) My question is how to do this most efficiently using gridspec or if there is another feature that makes such a setup a much easier task. I think I can add more columns and rows to the gridspec and custom define row height and column width ratios to recreate the plot but that seems like it would take a lot of trial and error on my part. Likewise if I were to define multiple gridspecs and define their layouts with the gridspec.update command would take some guessing and checking. A gridspec within a gridspec using GridSpecFromSubPlot command might be able to work but it doesn't have an attribute .update() to customize the wspace between plots in the gridspec that I know of. Is there a way to define a plots origin (in pixel or some other coordinates) and its extent? Thanks in advance! -- Matthew Bradley

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Re: [Matplotlib-users] True 3D plotting with matplotlib
by Ludwig Schwardt June 6, 2018

June 6, 2018

Hi, On the topic of publication-quality 3D vector graphics (but unfortunately not matplotlib...): I like Sketch. Although a bit old by now, you can still get it from sketch4latex.sourceforge.net. It has a bit of a learning curve (similar to TikZ) but is nice for basic 3D plots. I even used it to make a very basic vector animation viewable with Adobe Acrobat Reader (see slide 16 of the presentation at http://www.atnf.csiro.au/people/ban115/conferences/CALIM2014/talks/day3/cal… - will send source if interested). Good luck, Ludwig

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How to improve the speed of display implemented using matplotlib
by aishwarya selvaraj June 5, 2018

June 5, 2018

Hi all, I have 2 files created, one a .pyx file with a class named AndorCamersSDK which has a function named LiveAcquisition(). The second file, a .py file with a Class AndorCameraGUI which makes use of Tkinter to create a GUI. This class has function LivePlot(), and RepeatPlot().Inside LiveAcquisition() I am acquiring N number of frames and after acquiring each frame I need to display it using LivePlot() and RepeatPlot(). Without the display, just acquiring and storing for 300 frames takes 6.2 for execution, which is fine by me. But When I start displaying even for 100 frames it takes 54sec. I need to acquire and display within 6 sec for 300 frames. How do I solve this? File 1: .pyx code ; Present inside class AndorCameraSDK def LiveAcquisition(self): for i in range(no_of_frames): data[i,:,:] = PyArray_NewFromDescr(<PyTypeObject *> np.ndarray, np.dtype('<H'), 2,dims, strides,pBuf, np.NPY_C_CONTIGUOUS, None) if (i==0): self.master.LivePlot(data[i,:,:]) elif (i==2) or (i==15) or (i ==65) or (i ==96): self.master.RepeatPlot(data[i,:,:]) else: pass File 2 : .py code; Below functions are present inside a class named AndorCameraGUI def LivePlot(self,image): self.count = 0 self.fig = Figure(figsize = (4, 5)) self.fig.patch.set_facecolor('xkcd:light grey') # When this is removed a white color is seen in the background of the figure self.a = self.fig.add_subplot(111) self.a.set_xlim([0, self.image_width/int(self.HBin)]) self.a.set_ylim([0, self.image_height/int(self.VBin)]) image = image.transpose() self.a.imshow(image,'gray') self.canvas = FigureCanvasTkAgg(self.fig,self.master) self.canvas.draw() self.canvas.get_tk_widget().pack(side =LEFT) self.toolbar = NavigationToolbar2TkAgg(self.canvas,self.master) self.toolbar.update() self.canvas._tkcanvas.pack(side = LEFT)# change this to TOP so thee the navigation toolbar on the left down def RepeatPlot(self,image): image = image.transpose() self.a.imshow(image,'gray') self.canvas.draw() -- Regards, Aishwarya Selvaraj

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True 3D plotting with matplotlib
by clemens.loschnauer＠cantab.net June 3, 2018

June 3, 2018

Hi everyone, I have got a question with regards to the 3D plotting capabilites of matplotlib: Are there any plans/ongoing projects to make matplotlib (or its mplot3d submodule) suitable for complex 3D plotting? In particular, I am interested in plotting of geometric objects and surfaces and exporting these to vector graphics formats. I have done some research online and while there are some packages out there for 3D visualisation of data, all of them only export to raster graphics. The only program that I have come across that supports this is Mathematica, which is commercial. I believe that the option of producing publication-quality vector graphics for complex 3D scenes as might be desired in a scientific application is a feature that is currently missing in matplotlib. When I say high quality I have something like the 3D plots of the tikz/pgfplots packages in latex in mind, although again these do not support complex 3D scenes. I know there is mayavi, but I feel this does not offer the same quality for a scientific visualisation. Besides, it is a separate package and not part of matplotlib. An example of a visualisation that I want to achieve is the following: Plot a function of two variables as a 3D surface and then add a sphere that is tangent to the surface at some point. Then allow different camera angles with correct occlusion of hidden parts and varying levels of transparency. Add lighting and shading and export this as a vector graphic to a pdf file. Are there any plans to make something like this possible in matplotlib? If not, does anyone have hints as to what would be required to program this?

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Creating a smooth surface in 3D
by Bala subramanian June 3, 2018

June 3, 2018

Dear mpl friends, My objective is to create a molecular surface using matplotlib. I used the snippet pasted below to create a series of spheres (attached png), drawn using the atom attributes (their positions and radius). From here, I would like to create a smooth surface which can depict the shape of the molecule surface (curves,cavities etc). Based on examples in net, I get a mixed feeling that either triangulation or making 3D grids are some directions to proceed. If anyone has some suggestions or better protocols for such task with some example data, it would be of great help to me. fig = plt.figure(figsize=(6,6),dpi=140) ax1 = fig.add_subplot(111, projection='3d') # Define spherical coordinates u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j] S = np.cos(u)*np.sin(v) C = np.sin(u)*np.sin(v) T = np.cos(v) for P,R in zip(positions,radii): ax1.plot_wireframe(R*S+P[0],R*C+P[1],R*T+P[2],color='r',alpha=0.4) Thanks in advance, Bala -- C. Balasubramanian

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clip a surface data
by Bala subramanian June 3, 2018

June 3, 2018

Dear mpl friends, I have made a surface plot (attached) using trisurf. I want to remove from a part of the data from the view (encircled in the figure) so that the interior surface could be visible. Is there any facility available in mpl for the same. Just like making the front part invisible. I see functions like clip_path or clip_box etc, but from the documentation it is not clear for me to handle them. Any examples could be of much help. Thanks in advance, Bala -- C. Balasubramanian

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