11.1. Plotting in XmGrace

A high-level Python interface to the Grace plotting package XmGrace

• One line command plotting: plot of numpy arrays and dataArrays without predefining Data or Symbol objects.

• symbol, line and error are defined by list arguments as line=[1,0.5,3]

• Older functionality still works and can be used for more sophisticated output.

Resources

• XmGrace

• Deutschsprachiges Benutzerhandbuch und FAQ

Example

import jscatter as js
data=js.dL(js.examples.datapath+'/iqt_1hho.dat')               #read data from test directory into dataList
# open plot with fixed size of 2x3 inch or 2*300x3*300 pixel
p=js.grace(2,1)
p.multi(1,2)
#
p[0].plot(data[:8:2],symbol=[-1,1,-1,''],line=[1,2,''],legend='Q=$q')
p[1].plot(data[1:8:2],sy=[-1,1,-1],li=-1, legend='Q=$q')
#
 # make axes, legend, title, and subtitle to get nice plot
p[0].yaxis(min=0.09,max=1.1,scale='l',label='I(Q,t)/I(Q,0)',charsize=1.50,ticklabel=['power',0,1.3])
p[0].xaxis(min=0.0,max=150,label='fouriertime t / ns ',charsize=1.50)
p[1].xaxis(min=0.9,max=150,scale='log',label='fouriertime t / ns ',charsize=1.50)
p[0].legend(x=110,y=1)
p[0].title(r'An example for the intermediate scattering function in \n Neutron Spinecho Spectroscopy',size=1)
p[0].title('This is GraceGraph 1',size=2)
p[1].title('This is GraceGraph 2',size=2)
p[0].subtitle('colors of lines are sync to symbol color')
# add a text
p[1].text(r'Here we place a text just as demo\n at the last point of this dataset',x=1.2,y=0.3,charsize=1)
# p.save('testdata.agr') #as grace file
# p.save(js.examples.imagepath+'/Graceexample.jpg',format='jpeg',size=[2,1.33]) #as jpg file

some examples using GracePlot

Above; Smoothed Xray ; multilamellarVesicles()

Originally, this code of GracePlot started out from: Nathaniel Gray <n8gray@caltech.edu>, updated by Marcus H. Mendenhall, MHM ,John Kitchin, Marus Mendenhall

• original source -> sourceforge.net/projects/graceplot/ 2014 and according to that site: License: GNU General Public License version 2.0 (GPLv2)

• Consequently this file is still under GNU General Public License version 2.0 (GPLv2)

• 2019 changed some things to be only python 3 compatible

Ralf Biehl JCNS1 & ICS1 Forschungszentrum Juelich 2014-2019

11.1.1. GracePlot

GracePlot([width, height, auto_redraw, ...])

Open a Figure that will contain several graceGraph.

---

GracePlot.plot(*args, **kwargs)	Shortcut for sending the command directly to the appropriate graceGraph object see below
GracePlot.multi(rows, cols[, offset, hgap, vgap])	Create a grid of graphs with the given number of <rows> and <cols>
GracePlot.new_graph(**kwargs)	Add a new graph to plot.
GracePlot.stacked(number, hshift, vshift[, ...])	Creates a stacked chart with shifted graphs in the frame
GracePlot.clear(*args, **kwargs)	Shortcut for sending the command to current graceGraph see below
GracePlot.exit()	Nuke the grace session.
GracePlot.legend(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.save(filename[, size, dpi, format])	Save the current plot.
GracePlot.subtitle(*args, **kwargs)	Shortcut for sending the command to current graceGraph see below
GracePlot.text(*args, **kwargs)	Writes text to graph at specified position.
GracePlot.title(*args, **kwargs)	Shortcut for sending the command to current graceGraph see below
GracePlot.updateall()	Update the GUI (graph and set selectors etc) to reflect the current project state
GracePlot.write(command)	Make a graceSession look like a file, and flush after send
GracePlot.xaxis(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.xlabel(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.xlimit(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.yaxis(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.ylabel(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.ylimit(*args, **kwargs)	Shortcut for sending the command to current graceGraph
GracePlot.aspect_scale(x, y)	scale view coordinates to that (1,1) fills view, roughly
GracePlot.assign_color(idx, rgb, name)	Assign color to an index including new colors.
GracePlot.close()	Closes the plot
GracePlot.command_args
GracePlot.focus([graph_index, grace_graph])	Direct commands sent to the GracePlot to the appropriate GraceGraph.
GracePlot.grace_command
GracePlot.hold(*args, **kwargs)	Shortcut for sending the command to current graceGraph see below
GracePlot.is_open()	Return True if the pipe is not known to have been closed.
GracePlot.load_parameter_file(param_file_name)	load a grace *.par file
GracePlot.redraw([force, soon])	Refresh the plot
GracePlot.resetlast()	Resets last used symbols and lines.
GracePlot.resize(xdim, ydim)	Change the page dimensions (in pixel)for plots with fixed size.
GracePlot.resolution	resolution of the plot
GracePlot.send_commands(*commands)	Send a list of commands, and then flush

11.1.2. GraceGraph

GraceGraph.autoscale([axis])	autoscales axes
GraceGraph.autotick()
GraceGraph.clear([slice, hold])	Clear plot
GraceGraph.frame([type, linestyle, ...])	Set frame type of graph
GraceGraph.gen_axis(axis_prefix[, ax_min, ...])	Format of axis
GraceGraph.grace()
GraceGraph.hold([onoff])	Turn on/off overplotting for this graph.
GraceGraph.kill()	Kill the plot
GraceGraph.legend([strings, x, y, boxcolor, ...])	Place the legend in the plot or update it.
GraceGraph.line([x1, y1, x2, y2, linewidth, ...])	Draws line/arrow in plot.
GraceGraph.plot(*datasets, **kwargs)	Plot data in xmgrace
GraceGraph.redraw(*args, **kwargs)	redraw Graph
GraceGraph.resetlast()	Resets last used symbols and lines.
GraceGraph.subtitle([subtitle, font, size, ...])	Sets the graph subtitle
GraceGraph.text([string, x, y, color, rot, ...])	Writes text to graph at specified position.
GraceGraph.title([title, font, size, color])	Sets the graph title.
GraceGraph.update_data(set_index[, new_x, ...])	Efficiently update the data for a given data set.
GraceGraph.xaxis([min, max])	Format of axis
GraceGraph.xlabel(label[, charsize])	Convenience function to set the xaxis label charsize detemines charsize, default 1
GraceGraph.xlimit([lower, upper])	Convenience function to set the lower and/or upper bounds of the x-axis.
GraceGraph.yaxis([min, max])	Format of axis
GraceGraph.ylabel(label[, charsize])	Convenience function to set the yaxis label
GraceGraph.ylimit([lower, upper])	Convenience function to set the lower and/or upper bounds of the y-axis.
GraceGraph.SetView([xmin, ymin, xmax, ymax, ...])	this sets the viewport coords so they are available later for translating string and line coords.

11.1.3. Helper Classes

Annotation([onoff, type, charsize, font, ...])	controls annotation
Bar([axis, onoff, color, linestyle, linewidth])	this class controls the x and y bars in the frame apparently usually it is off onoff is 'on' or 'off' the rest are like everything else
Data([x, y, symbol, line, legend, comment, ...])	Simplest base class for all GracePlot data objects.
DataBar([x, y, symbol, line, legend, ...])
DataXYBoxWhisker(x, y, whisker_down, ...)	A data set with a box for an asymmetrical inner error in the 'y' direction and an error bar (whisker) for the asymmetrical outer error bound.
DataXYDX(x, y, dx, **kwargs)	A data set with symmetrical error bars in the 'x' direction
DataXYDXDX(x, y, dx_left, dx_right, **kwargs)	A data set with asymmetrical error bars in the 'x' direction
DataXYDXDXDYDY(x, y, dx_left, dx_right, ...)	A data set with asymmetrical error bars in the 'x' and 'y' direction
DataXYDXDY(x, y, dx, dy, **kwargs)	A data set with symmetrical error bars in the 'x' and 'y' direction
DataXYDY(x, y, dy, **kwargs)	A data set with symmetrical error bars in the 'y' direction
DataXYDYDY(x, y, dy_down, dy_up, **kwargs)	A data set with asymmetrical error bars in the 'y' direction
DataXYZ(x, y, z, **kwargs)
Errorbar([onoff, place, color, pattern, ...])	class for errorbars
Label([string, layout, place, charsize, ...])	Used for labels of the x-axis and y-axis
Line([type, linestyle, linewidth, color, ...])	Line objekt
Symbol([type, symbol, size, color, pattern, ...])	Symbol object
Tick([axis, onoff, major, minorticks, ...])	Controls appearence of ticks on an axis.
TickLabel([axis, onoff, type, prec, format, ...])	Ticklabels
colors
fills()
frames()
lines()
symbols()
Disconnected	Thrown when xmgrace unexpectedly disconnects from the pipe.
inheritDocstringFrom(cls)
on_off(flag)	convert a bool into an xmgrace on/off string

---

A high-level Python interface to the Grace plotting package XmGrace

• One line command plotting: plot of numpy arrays and dataArrays without predefining Data or Symbol objects.

• symbol, line and error are defined by list arguments as line=[1,0.5,3]

• Older functionality still works and can be used for more sophisticated output.

Resources

• XmGrace

• Deutschsprachiges Benutzerhandbuch und FAQ

Example

import jscatter as js
data=js.dL(js.examples.datapath+'/iqt_1hho.dat')               #read data from test directory into dataList
# open plot with fixed size of 2x3 inch or 2*300x3*300 pixel
p=js.grace(2,1)
p.multi(1,2)
#
p[0].plot(data[:8:2],symbol=[-1,1,-1,''],line=[1,2,''],legend='Q=$q')
p[1].plot(data[1:8:2],sy=[-1,1,-1],li=-1, legend='Q=$q')
#
 # make axes, legend, title, and subtitle to get nice plot
p[0].yaxis(min=0.09,max=1.1,scale='l',label='I(Q,t)/I(Q,0)',charsize=1.50,ticklabel=['power',0,1.3])
p[0].xaxis(min=0.0,max=150,label='fouriertime t / ns ',charsize=1.50)
p[1].xaxis(min=0.9,max=150,scale='log',label='fouriertime t / ns ',charsize=1.50)
p[0].legend(x=110,y=1)
p[0].title(r'An example for the intermediate scattering function in \n Neutron Spinecho Spectroscopy',size=1)
p[0].title('This is GraceGraph 1',size=2)
p[1].title('This is GraceGraph 2',size=2)
p[0].subtitle('colors of lines are sync to symbol color')
# add a text
p[1].text(r'Here we place a text just as demo\n at the last point of this dataset',x=1.2,y=0.3,charsize=1)
# p.save('testdata.agr') #as grace file
# p.save(js.examples.imagepath+'/Graceexample.jpg',format='jpeg',size=[2,1.33]) #as jpg file

some examples using GracePlot

Above; Smoothed Xray ; multilamellarVesicles()

Originally, this code of GracePlot started out from: Nathaniel Gray <n8gray@caltech.edu>, updated by Marcus H. Mendenhall, MHM ,John Kitchin, Marus Mendenhall

• original source -> sourceforge.net/projects/graceplot/ 2014 and according to that site: License: GNU General Public License version 2.0 (GPLv2)

• Consequently this file is still under GNU General Public License version 2.0 (GPLv2)

• 2019 changed some things to be only python 3 compatible

Ralf Biehl JCNS1 & ICS1 Forschungszentrum Juelich 2014-2019

class jscatter.graceplot.Annotation(onoff=True, type=None, charsize=None, font=None, color=None, rot=None, format=None, prec=None, prepend=None, append=None, offset=None)

Bases: object

controls annotation

Parameters:

onoff‘on’ or ‘off’

typeint

charsizefloat

fontint

colorint

rotfloat

formatint

precint

prependint

appendint

offsetint

output(dataset)

list output to sent to grace

class jscatter.graceplot.Bar(axis=None, onoff=True, color=None, linestyle=None, linewidth=None)

Bases: object

this class controls the x and y bars in the frame apparently usually it is off onoff is ‘on’ or ‘off’ the rest are like everything else

output(axis)

list output to sent to grace

class jscatter.graceplot.Data(x=None, y=None, symbol=None, line=None, legend='', comment=None, errorbar=None, pairs=None, dylist=None, **kwargs)

Bases: object

Simplest base class for all GracePlot data objects.

dataset_type_name = 'xy'

output(graceGraph, count)

No checking is done to make sure the datasets are consistent with each other, same number of x and y etc… Support of None values is only in the xy graph.

output_differences(graceGraph, count, new_x, new_y, new_dylist)

output strings to modify already created datasets, issuing results only for changed items

x_format_string = '%s'

y_format_string = '%s'

class jscatter.graceplot.DataBar(x=None, y=None, symbol=None, line=None, legend='', comment=None, errorbar=None, pairs=None, dylist=None, **kwargs)

Bases: Data

dataset_type_name = 'bar'

class jscatter.graceplot.DataXYBoxWhisker(x, y, whisker_down, box_down, whisker_up, box_up, **kwargs)

Bases: Data

A data set with a box for an asymmetrical inner error in the ‘y’ direction and an error bar (whisker) for the asymmetrical outer error bound. The symbol properties set the color (etc.) of the box. The errorbar properties set the color (etc.) of the whisker

dataset_type_name = 'xyboxplot'

class jscatter.graceplot.DataXYDX(x, y, dx, **kwargs)

Bases: Data

A data set with symmetrical error bars in the ‘x’ direction

dataset_type_name = 'xydx'

class jscatter.graceplot.DataXYDXDX(x, y, dx_left, dx_right, **kwargs)

Bases: Data

A data set with asymmetrical error bars in the ‘x’ direction

dataset_type_name = 'xydxdx'

class jscatter.graceplot.DataXYDXDXDYDY(x, y, dx_left, dx_right, dy_down, dy_up, **kwargs)

Bases: Data

A data set with asymmetrical error bars in the ‘x’ and ‘y’ direction

dataset_type_name = 'xydxdxdydy'

class jscatter.graceplot.DataXYDXDY(x, y, dx, dy, **kwargs)

Bases: Data

A data set with symmetrical error bars in the ‘x’ and ‘y’ direction

dataset_type_name = 'xydxdy'

class jscatter.graceplot.DataXYDY(x, y, dy, **kwargs)

Bases: Data

A data set with symmetrical error bars in the ‘y’ direction

dataset_type_name = 'xydy'

class jscatter.graceplot.DataXYDYDY(x, y, dy_down, dy_up, **kwargs)

Bases: Data

A data set with asymmetrical error bars in the ‘y’ direction

dataset_type_name = 'xydydy'

class jscatter.graceplot.DataXYZ(x, y, z, **kwargs)

Bases: Data

dataset_type_name = 'xyz'

exception jscatter.graceplot.Disconnected

Bases: Exception

Thrown when xmgrace unexpectedly disconnects from the pipe.

This exception is thrown on an EPIPE error, which indicates that xmgrace has stopped reading the pipe that is used to communicate with it. This could be because it has been closed (e.g., by clicking on the exit button), crashed, or sent an exit command.

class jscatter.graceplot.Errorbar(onoff=True, place=None, color=None, pattern=None, size=None, linewidth=None, linestyle=None, riserlinewidth=None, riserlinestyle=None, riserclip=None, risercliplength=None)

Bases: object

class for errorbars

Parameters:

onoffTrue False,’on’,’off’, default on

turns the error bars on or off

place‘normal’, ‘opposite’, ‘both’ default ‘both’

colorint

color integer

patternint

linewidthfloat

linestyleint

riserlinewidthfloat

risers are the lines from the symbol to the end

riserlinestyleint

riserclip‘on’,’off’

set to on or off, determines if an arrow is drawn for error bars offscale

risercliplengthfloat

output(symbol)

list output to sent to grace

class jscatter.graceplot.GraceGraph(grace, gID, xmin=0.15, xmax=0.95, ymin=0.15, ymax=0.9)

Bases: object

class for handling GraceGraph

Parameters:

gIDinteger

Graph ID

xmin,xmax,ymin,ymaxfloat default 0.15,0.95,0.15,0.88

position of edges in plot in relative view coordinates

Autoscale(axis=None)

autoscales axes

axis‘x’,’y’,None

None, scale all axes, otherwise if it is ‘x’ or ‘y’ scale that axis

Clear(slice=slice(None, None, None), hold=0)

Clear plot

Parameters:

sliceslice

Selects elements to delete. If ommited clear all. e.g. last for elements slice=slice(-4) don’t use slice extensivly as it could mess up.

holdbool, default 0

Set/reset to hold lines.

Legend(strings=None, x=None, y=None, boxcolor=None, boxpattern=None, boxlinewidth=None, boxlinestyle=None, boxfillcolor=None, boxfillpattern=None, font=None, charsize=None, color=None, length=None, vgap=None, hgap=None, invert=None, world_coords=True, offset=0, onoff=True, position=None)

Place the legend in the plot or update it.

Parameters:

stringslist of strings,string, default=None

List of legend strings or one string. If None then self.legend_strings is used. self.legend_strings is build from legend attribute in plot

offsetint, default 0

Which legend string to change if strings is single string >0 with offset shifted =<0 starting from last reverse order default 0 names last legend

x,y: float

Position of the upper left corner of the box in data coordinates

boxcolorint

Color of the legend box lines

boxpatterninteger

Pattern of the legend box lines

boxlinewidthfloat

Thickness of the line

boxlinestyle,boxfillcolor,boxfillpatterninteger

As name says

fontint

Is the font used in the legend

charsizefloat

Size of the characters

lengthint

Length of the box must be an integer

vgapint

Vertical space between entries, can be a float

hgapfloat

Horizontal spacing in the box can be a float

invertbool, (True,False)

Order of entries, either in the order they are entered, or the opposite

onoffbool

Show legend or not

position‘ll’, ‘ur’, ‘ul’, ‘lr’

Legend position shortcut. Shortcuts for lower left, upper right, upper left, lower right.

Plot(*datasets, **kwargs)

Plot data in xmgrace

e.g. p.plot(data,legend=’description’,symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])

Parameters:

datasetsdataArray, dataList,numpy array, lists of them

Several of (comma separated) nonkeyword arguments or as list. If dimension of datasets is one a new Data object is created and plotted see Notes below for error plots.

symbol,syint, list of float or Symbol object

• [symbol,size,color,fillcolor,fillpattern,linewidth] as [1,1,1,-1,2];

• single integer to chose symbol e.g.symbol=3; symbol=0 switches off

• negative increments from last, non integer repeat last

• symbol => 0-11 = ◦,☐,♢,▵,◁,▽,▷,+,×,☆,(11 is char)

• size => size, a number e.g.0.5

• color => int 0-16 = white,black,red,green,blue,ligth green,brown,

  darkgrey,violet,orange,magenta,grey

• fillcolor=None set color and adds fillpattern=1,

  non-integer syncs to symbol color

• fillpattern=None 0 empty, 1 full, ….test it

• linewidth 0.1-10 width of line for open symbols.

line,liint, list of float or Line object

• [linestyle,linewidth,color] as [1,1,’’];

• negative increments;non integer as ‘’ repeats last

• single integer to chose line line=1; line=0 switches of

• linestyle int 1 normal, 2 dotted, 3 dashed, 4 long dashed, 5 dot-dashed

• linewidth float goes from 0 to 6 in increasing thickness

• color see symbol color, non-integer syncs to symbol color

errorbar,erint or list of float or Errorbar object

• [color,size,linewidth,riserlinewidth] as [1,1,1,1]; no increment, no repeat

• color int see symbol color, non-integer syncs to symbol color

• size float default 1.0 ; smaller is 0.5

• linewidth float default 1.0

• riserlinewidth float default 1.0

legend,lestring

• determines legend for all datasets

• string replacement: attr name prepended by ‘$’ (eg. ‘$par’) is replaced by value str(par1.flatten()[0]) if possible. $(par) for not unique names

comment: string

• string determines comment for all datasets

• for dataArray: list of attribute values is set as comment to ckeck use dataArray.resumeAttrTxt()

autoscalebool

default True, False

internal_autoscalebool

default True, False 10% border

redrawbool

redraw

Notes

Plot types determined by dimension of dataset

• 1: dataset is type Data instances

  See Data class for possibilities and original documentation.

• 2: dataset is numpy array; simplified version

  Use slices like data_in_numpyarray[[0,3,2],:] to select columns to plot

  • len(array)= 2 XY

  • len(array)= 3 XYDY

  • len(array)= 4 XYDXDY

• 3: dataset is dataArray ; simplified version

  • attributes X,Y,eY,eX determine plot type if they exist. So set these before plot by dataset.setColumnIndex(3,4,7)

  • default is 0,1,2 for X,Y,eY, No eX

  • Slicing works too as for arrays.

For more complex plots use original Data class in 1. Old style plotting needs creation of GracePlot.Data objects like

d1=Data(x=x,y=y,symbol=GracePlot.Symbol(symbol=circle,fillcolor=red),line=GracePlot.Line(type=none))
or in short abreviation:
d1=Data(x=x,y=y,symbol=[-1,2,3,4],line=[1,2,3])
#plotted sets can be accessed by
p[0].datasets   as a list of Data objects

Examples

tX =np.r_[0:10]
tY=np.sin(tX)
data=np.c_[tX,tY,tY*0.05].T
p=s.grace()                    # open plot
# plot single column data tX,tY,teY
p.plot(tX,tY,legend='all 1D data',symbol=3,line=1,errorbar=[0])
#plot Data with arrray or dataList
p.plot(data,legend='description',symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])
p.yaxis(label='whatever / m')  # change y label
p.legend()                     # show legends

SetView(xmin=None, ymin=None, xmax=None, ymax=None, aspect_scaled=True)

this sets the viewport coords so they are available later for translating string and line coords.

Parameters:

xmin,xmax,ymin,ymaxfloat

view range

aspect_scaledbool

aspect

Subtitle(subtitle=None, font=None, size=None, color=None)

Sets the graph subtitle

see title

Title(title=None, font=None, size=None, color=None)

Sets the graph title.

Parameters:

titlestring

Title string

font

Font of title

sizefloat

Size of title

colorinteger

Color of title

Xaxis(min=None, max=None, **kwargs)

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

Yaxis(min=None, max=None, **kwargs)

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

autoscale(axis=None)

autoscales axes

axis‘x’,’y’,None

None, scale all axes, otherwise if it is ‘x’ or ‘y’ scale that axis

autotick()

clear(slice=slice(None, None, None), hold=0)

Clear plot

Parameters:

sliceslice

Selects elements to delete. If ommited clear all. e.g. last for elements slice=slice(-4) don’t use slice extensivly as it could mess up.

holdbool, default 0

Set/reset to hold lines.

frame(type=None, linestyle=None, linewidth=None, color=None, pattern=None, backgroundcolor=None, backgroundpattern=None)

Set frame type of graph

Parameters:

type[0,1,2,3,4,5] => closed,halfopen,breaktop,breakbottom,breakleft,breakright

Boxtype

linestyleint

Linestyle; see plot

linewidthfloat

linewidth; see plot

colorint; see plot

Color

patternint

Pattern

backgroundcolorint

Color

backgroundpatternint

Pattern

Notes

For the different types except of close the axis bar and tick marks need to be removed

gen_axis(axis_prefix, ax_min=None, ax_max=None, scale=None, invert=None, formula=None, offset=None, label=None, ticklabel=None, charsize=None, size=None, tick=None, bar=None, autotick=True)

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

grace()

hold(onoff=None)

Turn on/off overplotting for this graph.

Call as hold() to toggle, hold(1) to turn on, or hold(0) to turn off. Returns the previous hold setting.

kill()

Kill the plot

legend(strings=None, x=None, y=None, boxcolor=None, boxpattern=None, boxlinewidth=None, boxlinestyle=None, boxfillcolor=None, boxfillpattern=None, font=None, charsize=None, color=None, length=None, vgap=None, hgap=None, invert=None, world_coords=True, offset=0, onoff=True, position=None)

Place the legend in the plot or update it.

Parameters:

stringslist of strings,string, default=None

List of legend strings or one string. If None then self.legend_strings is used. self.legend_strings is build from legend attribute in plot

offsetint, default 0

Which legend string to change if strings is single string >0 with offset shifted =<0 starting from last reverse order default 0 names last legend

x,y: float

Position of the upper left corner of the box in data coordinates

boxcolorint

Color of the legend box lines

boxpatterninteger

Pattern of the legend box lines

boxlinewidthfloat

Thickness of the line

boxlinestyle,boxfillcolor,boxfillpatterninteger

As name says

fontint

Is the font used in the legend

charsizefloat

Size of the characters

lengthint

Length of the box must be an integer

vgapint

Vertical space between entries, can be a float

hgapfloat

Horizontal spacing in the box can be a float

invertbool, (True,False)

Order of entries, either in the order they are entered, or the opposite

onoffbool

Show legend or not

position‘ll’, ‘ur’, ‘ul’, ‘lr’

Legend position shortcut. Shortcuts for lower left, upper right, upper left, lower right.

line(x1=None, y1=None, x2=None, y2=None, linewidth=None, linestyle=None, color=None, arrow=None, arrowtype=None, arrowlength=None, arrowlayout=None, world_coords=True)

Draws line/arrow in plot.

Parameters:

x1,y1,x2,y2float

Start and end point. Coordinates are the cartesian cooridinates for a single graph.

linewidthfloat

Width

linestyleint

Style

colorint

Color

arrowint

Tells where the arrowhead is and is 0,1,2, or 3 for none, start, end, both ends

arrowtypeint

Is for line (0), filled (1), or opaque (2), and only have an effect if the arrowlayout is not (1,1)

arrowlayout[int,int]

Must be a list of 2 numbers, arrowlayout=(1,1) the first number relates to d/L and the second is I/L the meaning of which is unclear, but they affect the arrow shape.

plot(*datasets, **kwargs)

Plot data in xmgrace

e.g. p.plot(data,legend=’description’,symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])

Parameters:

datasetsdataArray, dataList,numpy array, lists of them

Several of (comma separated) nonkeyword arguments or as list. If dimension of datasets is one a new Data object is created and plotted see Notes below for error plots.

symbol,syint, list of float or Symbol object

• [symbol,size,color,fillcolor,fillpattern,linewidth] as [1,1,1,-1,2];

• single integer to chose symbol e.g.symbol=3; symbol=0 switches off

• negative increments from last, non integer repeat last

• symbol => 0-11 = ◦,☐,♢,▵,◁,▽,▷,+,×,☆,(11 is char)

• size => size, a number e.g.0.5

• color => int 0-16 = white,black,red,green,blue,ligth green,brown,

  darkgrey,violet,orange,magenta,grey

• fillcolor=None set color and adds fillpattern=1,

  non-integer syncs to symbol color

• fillpattern=None 0 empty, 1 full, ….test it

• linewidth 0.1-10 width of line for open symbols.

line,liint, list of float or Line object

• [linestyle,linewidth,color] as [1,1,’’];

• negative increments;non integer as ‘’ repeats last

• single integer to chose line line=1; line=0 switches of

• linestyle int 1 normal, 2 dotted, 3 dashed, 4 long dashed, 5 dot-dashed

• linewidth float goes from 0 to 6 in increasing thickness

• color see symbol color, non-integer syncs to symbol color

errorbar,erint or list of float or Errorbar object

• [color,size,linewidth,riserlinewidth] as [1,1,1,1]; no increment, no repeat

• color int see symbol color, non-integer syncs to symbol color

• size float default 1.0 ; smaller is 0.5

• linewidth float default 1.0

• riserlinewidth float default 1.0

legend,lestring

• determines legend for all datasets

• string replacement: attr name prepended by ‘$’ (eg. ‘$par’) is replaced by value str(par1.flatten()[0]) if possible. $(par) for not unique names

comment: string

• string determines comment for all datasets

• for dataArray: list of attribute values is set as comment to ckeck use dataArray.resumeAttrTxt()

autoscalebool

default True, False

internal_autoscalebool

default True, False 10% border

redrawbool

redraw

Notes

Plot types determined by dimension of dataset

• 1: dataset is type Data instances

  See Data class for possibilities and original documentation.

• 2: dataset is numpy array; simplified version

  Use slices like data_in_numpyarray[[0,3,2],:] to select columns to plot

  • len(array)= 2 XY

  • len(array)= 3 XYDY

  • len(array)= 4 XYDXDY

• 3: dataset is dataArray ; simplified version

  • attributes X,Y,eY,eX determine plot type if they exist. So set these before plot by dataset.setColumnIndex(3,4,7)

  • default is 0,1,2 for X,Y,eY, No eX

  • Slicing works too as for arrays.

For more complex plots use original Data class in 1. Old style plotting needs creation of GracePlot.Data objects like

d1=Data(x=x,y=y,symbol=GracePlot.Symbol(symbol=circle,fillcolor=red),line=GracePlot.Line(type=none))
or in short abreviation:
d1=Data(x=x,y=y,symbol=[-1,2,3,4],line=[1,2,3])
#plotted sets can be accessed by
p[0].datasets   as a list of Data objects

Examples

tX =np.r_[0:10]
tY=np.sin(tX)
data=np.c_[tX,tY,tY*0.05].T
p=s.grace()                    # open plot
# plot single column data tX,tY,teY
p.plot(tX,tY,legend='all 1D data',symbol=3,line=1,errorbar=[0])
#plot Data with arrray or dataList
p.plot(data,legend='description',symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])
p.yaxis(label='whatever / m')  # change y label
p.legend()                     # show legends

redraw(*args, **kwargs)

redraw Graph

pass through to our GraceGraph instance

resetlast()

Resets last used symbols and lines.

lastline=[1,0,0] lastsymbol=[1,0.5,1,0] lasterror=[0,0,0,0]

shiftbyfactor(xy=None, factor=None, repeat=None, scale='lin', xfactors=None, yfactors=None)

Shift data consecutively by factors

Consecutively multiply by 2 as 2,4,6,8…. or with power laws.

Parameters:

xy‘xy’

Selector for x or y axis or both

factorfloat

Shift factor

repeatfloat default=number of sets in plot

Repeat number of times the factor 3 -> 2,4,6,2,4,6… for factor=2

xfactorsarray or list

Factors as list, overrides factor and repeat

yfactorsarray or list

Factors as list,overrides factor and repeat dylist is also shifted

scale‘log’, other

If ‘log’ a factor**i is used for logarithmic scale all other factor*i is used

Notes

List is

factor*np.tile(np.r_[1:repeat+1],nSets)  lin scale
factor**np.tile(np.r_[1:repeat+1],nSets)  log scale

Create factors manually e.g. by

np.tile([1,2,3],3)         -->  array([1, 2, 3, 1, 2, 3, 1, 2, 3])
1.1**np.tile([1,1,2],3)    -->  array([1.1, 1.1, 1.21, 1.1, 1.1, 1.21, 1.1, 1.1, 1.21])
#for an inverse shifting
2*np.tile(np.r_[10:1:-1],3)-->  array([20, 18, 16, 14, 12, 10,  8,  6,  4, 20, 18, 16, 14, 12, 10,  8,  6, 4])

subtitle(subtitle=None, font=None, size=None, color=None)

Sets the graph subtitle

see title

text(string=None, x=None, y=None, color=None, rot=0, font=None, just=None, charsize=None, world_coords=True)

Writes text to graph at specified position.

Parameters:

stringstring

Text to print

x,y: float

Coordinates are the cartesian coordinates of x,y axis

colorint

Color

rotfloat

Rotation angle

fontint

Font as defined in default xmgrace plot

just

Justification

charsizefloat

Charsize

world_coordsbool

World coordinates or viewport coordinates

Notes

Try in Gui for values.

title(title=None, font=None, size=None, color=None)

Sets the graph title.

Parameters:

titlestring

Title string

font

Font of title

sizefloat

Size of title

colorinteger

Color of title

update_data(set_index, new_x=None, new_y=None, new_dylist=None)

Efficiently update the data for a given data set. set length, etc. must not change!

xaxis(min=None, max=None, **kwargs)

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

xlabel(label, charsize=None)

Convenience function to set the xaxis label charsize detemines charsize, default 1

xlimit(lower=None, upper=None)

Convenience function to set the lower and/or upper bounds of the x-axis.

yaxis(min=None, max=None, **kwargs)

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

ylabel(label, charsize=None)

Convenience function to set the yaxis label

ylimit(lower=None, upper=None)

Convenience function to set the lower and/or upper bounds of the y-axis.

class jscatter.graceplot.GracePlot(width=None, height=None, auto_redraw=True, redraw_interval=0.1, headless=False, size=None)

Bases: object

Open a Figure that will contain several graceGraph.

Default resolution is 300 dpi

Parameters:

widthfloat

Page width in inch, pixel width = width*resolution = width*300

heightfloat

Page height in inch, pixel height = height*resolution = height*300

auto_redrawbool

Redraw

redraw_intervalfloat

Time between redraw.

headlessbool

Use plot in nonGui mode (headless). Save Plot using save method and inspect later.

Returns:

GracePlotGracePlot instance

Notes

default resolution is 300 dpi

Create a GracePlot object, which manages an external grace instance. The instance may have multiple GraceGraph objects within it. Commands which are specific to a graph (such as plotting data) are sent to the graph object. Commanbds which are global (such as redraw control) are sent to the GracePlot object.

width*resolution=width in pixels, same for height. Resolution is set to 300 by default, so width is roughly inches on an 300 dpi monitor. By changing the class default resolution, you can change the units of width & height.

If auto_redraw is True, the graph will automatically hold off redrawing until data stops being sent for a time of redraw_interval (seconds).

To force an immediate redraw, call GracePlot.redraw(force=True). Calling GracePlot.redraw() without an argument schedules a redraw at the next quiet interval. This mechanism greatly reduces thrashing of grace windows by repeated un-needed redraws.

To force a redraw on the next cycle of the redrawing thread, call GracePlot.redraw(soon=True). This will cause a redraw even if there is still data flowing, but not in a hurry.

The GracePlot class does all its data transmission through a thread, so usually there should be no significant time during which the calling thread is blocked. This should improve real-time performance.

Clear(*args, **kwargs)

Shortcut for sending the command to current graceGraph see below

Clear plot

Parameters:

sliceslice

Selects elements to delete. If ommited clear all. e.g. last for elements slice=slice(-4) don’t use slice extensivly as it could mess up.

holdbool, default 0

Set/reset to hold lines.

Exit()

Nuke the grace session.

Multi(rows, cols, offset=0.13, hgap=0.1, vgap=0.15)

Create a grid of graphs with the given number of <rows> and <cols>

Arrange existing graphs (or add extra if needed) to form an nrows by ncols matrix, leaving offset at each page edge with hgap and vgap relative horizontal and vertical spacings

Parameters:

rows,colsinteger

Number of graphs

offsetfloat

Offset from edges

hgap,vgapfloat

Horizontal, vertical gap between plots

Notes

Overmuch graphs are deleted

Save(filename, size=(3.4, 2.4), dpi=300, format=None)

Save the current plot.

Parameters:

filenamestring

If filename has extension this is used instead of format.

size(float, float)

Size in inch. For PRL and other papers: Figures should be planned for the column width (8.4 cm or 3 3/8 = 3.4 in.) with 600 dpi:

• 150 dpi (ok in Powerpoint as png )

• 300 dpi (default) for fast printing

• 600 dpi (paper ready quality e.g. as eps, jpg or png)

svg or pdf are vector graphics and scale their resolution.

dpiin

Resolution in dots per inch (2.54 cm)

format : string x11, postscript, eps, pdf, mif, svg, pnm, jpeg, png, metafile

formatDefault is Grace ‘.agr’ file

‘agr’, ‘eps’, ‘jpeg’, ‘metafile’, ‘mif’, ‘pdf’, ‘png’, ‘pnm’, ‘postscript’, ‘svg’, ‘x11’

Notes

Not all drivers are created equal. For caveats that apply to some of these formats see the Grace documentation.

SetView(*args, **kwargs)

Shortcut for sending the command directly to the appropriate graceGraph object see below

this sets the viewport coords so they are available later for translating string and line coords.

Parameters:

xmin,xmax,ymin,ymaxfloat

view range

aspect_scaledbool

aspect

aspect_scale(x, y)

scale view coordinates to that (1,1) fills view, roughly

assign_color(idx, rgb, name)

Assign color to an index including new colors.

Parameters:

idxint (0..16..)

Index of color.

rgbset of integer (0..255)

RGB color as (0,0,0)

namestring

New name of color.

Notes

If used indices are changed the corresponding elements using this are changed too. This means changing index 1 (usually black) used for the axes changes axes color.

More can be used.

Examples

Set color 4 to (0, 0, 255) as blue

assign_color(4, (0,0,255), 'blue')

Append a list of new colors and use them in plot

x=np.r_[1:10]
p=js.grace()
p.colors.list    # shows actual color list
NN=40
clist=np.c_[np.r_[1:NN+1],np.r_[255:0:NN*1j].round(),np.r_[255:0:NN*1j].round(),np.r_[0:255:NN*1j].round()]
for i,r,g,b in clist:
   p.assign_color(i+15,(r,g,b),'test%.2g' %i)
for i in np.r_[1:p.colors.len]:
   p.plot(x,x+i,sy=[1,0.7,p.colors.len-i],li=[1,5,i])

reassign colors

clist=np.c_[np.r_[1:NN+1],np.r_[0:255:NN*1j].round(),np.r_[255:0:NN*1j].round(),np.r_[0:255:NN*1j].round()]
for i,r,g,b in clist:
   p.assign_color(i+15,(r,g,b),'test%.2g' %i)

reassign colors grey scale:

clist=np.c_[np.r_[1:NN+1],np.r_[0:255:NN*1j].round(),np.r_[0:255:NN*1j].round(),np.r_[0:255:NN*1j].round()]
for i,r,g,b in clist:
   p.assign_color(i+15,(r,g,b),'test%.2g' %i)

clear(*args, **kwargs)

Shortcut for sending the command to current graceGraph see below

Clear plot

Parameters:

sliceslice

Selects elements to delete. If ommited clear all. e.g. last for elements slice=slice(-4) don’t use slice extensivly as it could mess up.

holdbool, default 0

Set/reset to hold lines.

close()

Closes the plot

command_args = ('-nosafe', '-noask')

exit()

Nuke the grace session.

focus(graph_index=None, grace_graph=None)

Direct commands sent to the GracePlot to the appropriate GraceGraph.

Mostly for backwards compatibility. It is preferable to send the commands directly to the plot:

p[2].plot(....)

grace_command = 'xmgrace'

headless = False

hold(*args, **kwargs)

Shortcut for sending the command to current graceGraph see below

Turn on/off overplotting for this graph.

Call as hold() to toggle, hold(1) to turn on, or hold(0) to turn off. Returns the previous hold setting.

is_open()

Return True if the pipe is not known to have been closed.

legend(*args, **kwargs)

Shortcut for sending the command to current graceGraph

Place the legend in the plot or update it.

Parameters:

stringslist of strings,string, default=None

List of legend strings or one string. If None then self.legend_strings is used. self.legend_strings is build from legend attribute in plot

offsetint, default 0

Which legend string to change if strings is single string >0 with offset shifted =<0 starting from last reverse order default 0 names last legend

x,y: float

Position of the upper left corner of the box in data coordinates

boxcolorint

Color of the legend box lines

boxpatterninteger

Pattern of the legend box lines

boxlinewidthfloat

Thickness of the line

boxlinestyle,boxfillcolor,boxfillpatterninteger

As name says

fontint

Is the font used in the legend

charsizefloat

Size of the characters

lengthint

Length of the box must be an integer

vgapint

Vertical space between entries, can be a float

hgapfloat

Horizontal spacing in the box can be a float

invertbool, (True,False)

Order of entries, either in the order they are entered, or the opposite

onoffbool

Show legend or not

position‘ll’, ‘ur’, ‘ul’, ‘lr’

Legend position shortcut. Shortcuts for lower left, upper right, upper left, lower right.

load_parameter_file(param_file_name)

load a grace *.par file

multi(rows, cols, offset=0.13, hgap=0.1, vgap=0.15)

Create a grid of graphs with the given number of <rows> and <cols>

Arrange existing graphs (or add extra if needed) to form an nrows by ncols matrix, leaving offset at each page edge with hgap and vgap relative horizontal and vertical spacings

Parameters:

rows,colsinteger

Number of graphs

offsetfloat

Offset from edges

hgap,vgapfloat

Horizontal, vertical gap between plots

Notes

Overmuch graphs are deleted

new_graph(**kwargs)

Add a new graph to plot.

Parameters:

xmin,xmax,ymin,ymaxfloat; default 0.15,0.95,0.15,0.88

Position of edges in plot in relative view coordinates

plot(*args, **kwargs)

Shortcut for sending the command directly to the appropriate graceGraph object see below

Plot data in xmgrace

e.g. p.plot(data,legend=’description’,symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])

Parameters:

datasetsdataArray, dataList,numpy array, lists of them

Several of (comma separated) nonkeyword arguments or as list. If dimension of datasets is one a new Data object is created and plotted see Notes below for error plots.

symbol,syint, list of float or Symbol object

• [symbol,size,color,fillcolor,fillpattern,linewidth] as [1,1,1,-1,2];

• single integer to chose symbol e.g.symbol=3; symbol=0 switches off

• negative increments from last, non integer repeat last

• symbol => 0-11 = ◦,☐,♢,▵,◁,▽,▷,+,×,☆,(11 is char)

• size => size, a number e.g.0.5

• color => int 0-16 = white,black,red,green,blue,ligth green,brown,

  darkgrey,violet,orange,magenta,grey

• fillcolor=None set color and adds fillpattern=1,

  non-integer syncs to symbol color

• fillpattern=None 0 empty, 1 full, ….test it

• linewidth 0.1-10 width of line for open symbols.

line,liint, list of float or Line object

• [linestyle,linewidth,color] as [1,1,’’];

• negative increments;non integer as ‘’ repeats last

• single integer to chose line line=1; line=0 switches of

• linestyle int 1 normal, 2 dotted, 3 dashed, 4 long dashed, 5 dot-dashed

• linewidth float goes from 0 to 6 in increasing thickness

• color see symbol color, non-integer syncs to symbol color

errorbar,erint or list of float or Errorbar object

• [color,size,linewidth,riserlinewidth] as [1,1,1,1]; no increment, no repeat

• color int see symbol color, non-integer syncs to symbol color

• size float default 1.0 ; smaller is 0.5

• linewidth float default 1.0

• riserlinewidth float default 1.0

legend,lestring

• determines legend for all datasets

• string replacement: attr name prepended by ‘$’ (eg. ‘$par’) is replaced by value str(par1.flatten()[0]) if possible. $(par) for not unique names

comment: string

• string determines comment for all datasets

• for dataArray: list of attribute values is set as comment to ckeck use dataArray.resumeAttrTxt()

autoscalebool

default True, False

internal_autoscalebool

default True, False 10% border

redrawbool

redraw

Notes

Plot types determined by dimension of dataset

• 1: dataset is type Data instances

  See Data class for possibilities and original documentation.

• 2: dataset is numpy array; simplified version

  Use slices like data_in_numpyarray[[0,3,2],:] to select columns to plot

  • len(array)= 2 XY

  • len(array)= 3 XYDY

  • len(array)= 4 XYDXDY

• 3: dataset is dataArray ; simplified version

  • attributes X,Y,eY,eX determine plot type if they exist. So set these before plot by dataset.setColumnIndex(3,4,7)

  • default is 0,1,2 for X,Y,eY, No eX

  • Slicing works too as for arrays.

For more complex plots use original Data class in 1. Old style plotting needs creation of GracePlot.Data objects like

d1=Data(x=x,y=y,symbol=GracePlot.Symbol(symbol=circle,fillcolor=red),line=GracePlot.Line(type=none))
or in short abreviation:
d1=Data(x=x,y=y,symbol=[-1,2,3,4],line=[1,2,3])
#plotted sets can be accessed by
p[0].datasets   as a list of Data objects

Examples

tX =np.r_[0:10]
tY=np.sin(tX)
data=np.c_[tX,tY,tY*0.05].T
p=s.grace()                    # open plot
# plot single column data tX,tY,teY
p.plot(tX,tY,legend='all 1D data',symbol=3,line=1,errorbar=[0])
#plot Data with arrray or dataList
p.plot(data,legend='description',symbol=[1,0.5,4],line=[1,2,2],errorbar=[0])
p.yaxis(label='whatever / m')  # change y label
p.legend()                     # show legends

redraw(force=False, soon=False)

Refresh the plot

resetlast()

Resets last used symbols and lines.

lastline=[1,0,0] lastsymbol=[1,0.5,1,0] lasterror=[0,0,0,0]

resize(xdim, ydim)

Change the page dimensions (in pixel)for plots with fixed size.

Parameters:

xdim, ydimint

dimension in pixel

resolution = 300

resolution of the plot

save(filename, size=(3.4, 2.4), dpi=300, format=None)

Save the current plot.

Parameters:

filenamestring

If filename has extension this is used instead of format.

size(float, float)

Size in inch. For PRL and other papers: Figures should be planned for the column width (8.4 cm or 3 3/8 = 3.4 in.) with 600 dpi:

• 150 dpi (ok in Powerpoint as png )

• 300 dpi (default) for fast printing

• 600 dpi (paper ready quality e.g. as eps, jpg or png)

svg or pdf are vector graphics and scale their resolution.

dpiin

Resolution in dots per inch (2.54 cm)

format : string x11, postscript, eps, pdf, mif, svg, pnm, jpeg, png, metafile

formatDefault is Grace ‘.agr’ file

‘agr’, ‘eps’, ‘jpeg’, ‘metafile’, ‘mif’, ‘pdf’, ‘png’, ‘pnm’, ‘postscript’, ‘svg’, ‘x11’

Notes

Not all drivers are created equal. For caveats that apply to some of these formats see the Grace documentation.

send_commands(*commands)

Send a list of commands, and then flush

Parameters:

commandslist of strings

shiftbyfactor(*args, **kwargs)

Shortcut for sending the command directly to the appropriate graceGraph object see below

Shift data consecutively by factors

Consecutively multiply by 2 as 2,4,6,8…. or with power laws.

Parameters:

xy‘xy’

Selector for x or y axis or both

factorfloat

Shift factor

repeatfloat default=number of sets in plot

Repeat number of times the factor 3 -> 2,4,6,2,4,6… for factor=2

xfactorsarray or list

Factors as list, overrides factor and repeat

yfactorsarray or list

Factors as list,overrides factor and repeat dylist is also shifted

scale‘log’, other

If ‘log’ a factor**i is used for logarithmic scale all other factor*i is used

Notes

List is

factor*np.tile(np.r_[1:repeat+1],nSets)  lin scale
factor**np.tile(np.r_[1:repeat+1],nSets)  log scale

Create factors manually e.g. by

np.tile([1,2,3],3)         -->  array([1, 2, 3, 1, 2, 3, 1, 2, 3])
1.1**np.tile([1,1,2],3)    -->  array([1.1, 1.1, 1.21, 1.1, 1.1, 1.21, 1.1, 1.1, 1.21])
#for an inverse shifting
2*np.tile(np.r_[10:1:-1],3)-->  array([20, 18, 16, 14, 12, 10,  8,  6,  4, 20, 18, 16, 14, 12, 10,  8,  6, 4])

stacked(number, hshift, vshift, frame=None, yaxis='off', yaxisnumber=0, frametype=0, framepattern=1)

Creates a stacked chart with shifted graphs in the frame

Already exsiting graphs are reused, fineadjustement needs to be done by hand.

Parameters:

numberint

Number of graphs

hshiftfloat

Horizontal shift in viewport coords

vshiftfloat

Vertikal shift in viewport coords

yaxis‘normal’,’opposite’,’both’,default ‘off’

Where to place the yaxis

framepatternint

Frame pattern type; 1 is No frame

frame[float,float,float,float], default [0.15,0.15,0.9,0.9]

Frame size in viewport coordinates [0..1]

yaxisnumberint

Framenumber where to place yaxis

frametypeint

Frametype 0=closed,1=halfopen,2,3,4,5= break at top,bottom,left,right

framepattern

0= None, 1=full,…..and so on

Examples

p.stacked(10,hshift=0.02,vshift=0.01,yaxis='off')
p.stacked(10,hshift=-0.015,vshift=-0.01,yaxis='off')

#create a stacked chart of 10 plots
# each shifted by hshift,vshift
#the yaxis is switched off for all except the first
x=np.r_[0:5:100j]
p=js.grace()
p.stacked(10,hshift=0.02,vshift=0.01,yaxis='off')
#plot some Gaussians
for i in np.arange(10):p[i].plot(x,(i+1)*np.exp(-((x-2)*3)**2),li=[1,2,i+1],sy=0)
#choose the same yscale for the data but no ticks for the later plots
p.g[0].yaxis(min=0,max=10)
for pp in p.g[1:]:pp.yaxis(min=0,max=10,tick=False)
#adjusting the scale and the size of the xaxis ticks
for pp in p:pp.xaxis(tick=[1,1,0.3,0.1])
p[0].yaxis(tick=[1,1,0.3,0.1])

subtitle(*args, **kwargs)

Shortcut for sending the command to current graceGraph see below

Sets the graph subtitle

see title

text(*args, **kwargs)

Writes text to graph at specified position.

Parameters:

stringstring

Text to print

x,y: float

Coordinates are the cartesian coordinates of x,y axis

colorint

Color

rotfloat

Rotation angle

fontint

Font as defined in default xmgrace plot

just

Justification

charsizefloat

Charsize

world_coordsbool

World coordinates or viewport coordinates

Notes

Try in Gui for values.

title(*args, **kwargs)

Shortcut for sending the command to current graceGraph see below

Sets the graph title.

Parameters:

titlestring

Title string

font

Font of title

sizefloat

Size of title

colorinteger

Color of title

updateall()

Update the GUI (graph and set selectors etc) to reflect the current project state

write(command)

Make a graceSession look like a file, and flush after send

xaxis(*args, **kwargs)

Shortcut for sending the command to current graceGraph

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

xlabel(*args, **kwargs)

Shortcut for sending the command to current graceGraph

see below

Convenience function to set the xaxis label

charsize detemines charsize, default 1

xlimit(*args, **kwargs)

Shortcut for sending the command to current graceGraph

see below

Convenience function to set the lower and/or upper bounds of the x-axis.

yaxis(*args, **kwargs)

Shortcut for sending the command to current graceGraph

Format of axis

Parameters:

axis_prefix{‘x’,’y’}

determines axis

ax_min,ax_maxfloat

min and max of axis

scale{‘normal’, ‘logarithmic’, or ‘reciprocal’ or respectivly ‘n’,’l’,’r’}

sets type of axis

labelstring, list or Label object

Label of the axis; see Label object.

• string: this is the label string.

• list = [label string, charsize, place, color, location]

• place : ‘normal’,’both’,’opposite’

• location : [parallel, perpendicular] offset from axis center. defauls [0,0.08]

invert{True,False}

invert axis

formulagrace equation

formula for ticklabel calculation eg. for rescaling.

$t is label -> scaling as “$t*1e5”

charsize,sizefloat

determines character size, default 1

offsetlist of float

determines the position of the normal and opposite axis position

autotickbool

autoticking

tickTick object or list, False, True

list of [major tick distance , minorticks number, majorsize, minorsize, position]

• position as one of ‘normal’,’both’,’opposite’ (first letter is enough)

• False, True switch Ticks on and off

see Tick for more

ticklabelfloat, list, tickLabel object

With [format,precision,charsize,placeon] or a shortcut

• format: ‘decimal’,’exponential’,’general’,’power’,’scientific’

• precision : integer

• charsize : float

• placeon : ‘normal’,’both’,’opposite’

Shortcuts:

• ‘on’, ‘off’,1,0: switch ticklabel on/off

• float: used as charsize

• one of format strings: change format (‘power’,’scientific’ with precision=0’)

bar‘on’,’off’,list or bar object

list=[onoff,color,linestyle,linewidth]

See bar object. ‘on’/’off’ switch on or off.

ylabel(*args, **kwargs)

Shortcut for sending the command to current graceGraph

see below

Convenience function to set the yaxis label

ylimit(*args, **kwargs)

Shortcut for sending the command to current graceGraph

see below

Convenience function to set the lower and/or upper bounds of the y-axis.

class jscatter.graceplot.Label(string=None, layout=None, place=None, charsize=None, font=None, color=None, axis=None, location=None)

Bases: object

Used for labels of the x-axis and y-axis

output(axis)

list output to sent to grace

class jscatter.graceplot.Line(type=None, linestyle=None, linewidth=None, color=None, pattern=None, baselinetype=None, baseline=None, dropline=None)

Bases: object

Line objekt

Parameters:

type: int

0 None; 1 straigth; 2 left_stairs; 3 right_stairs; 4 Segments; 5 3-Segments

linestyleint

1 is normal; 2 is dotted; 3 is dashed; 4 is long dashed; 5 is dot-dashed

linewidthfloat

goes from 0 to 6 in increasing thickness

colorint

color

patternint

fill pattern 1 is solid, 0 is None, there are about 24 choices as dotted, dashed, squared.

baselineint

show baseline

baselinetypeint

0 Zero; 1 set min: 2 set max; 3 graph min: 4 graph max; 5 set average

dropline0,1

drop line to baseline

output(dataset)

list output to sent to grace

class jscatter.graceplot.Symbol(type=None, symbol=None, size=None, color=1, pattern=None, linewidth=None, linestyle=None, filltype=None, fillrule=None, fillcolor=None, fillpattern=None, char=None, charfont=None, skip=None, annotation=None, errorbar=None)

Bases: object

Symbol object

Parameters:

typeNone,’xy’,’xydy’,’xydxdy’,….,’bar’ ==> 0, 1, 2, 3, ….. 0

None is automatic determination inside grace

symbol(0..11)

0 None, 1 circle, 2 square, 3 diamond, 4 triangle up, 5 triangle left, 6 triangle down, 7 triangle right, 8 +, 9 x, 10 *, 11 character,

sizefloat

Self explanatory, 0.5 is 50 in the GUI

patternint 0-24

The pattern of the outline of the symbol, usually it will be 1

linewidthfloat

thickness of the outline of the symbol

linestyleint

0 None, 1 solid, 2 points, 3 broken line

fillcolorint

color the symbol is filled with, by default it is the same as the outline color.

fillpatternint, 0..24

pattern of the fill, 1 is solid, 0 is None, there are about 24 choices as dotted, dashed, squared.

output(dataset)

list output to sent to grace

class jscatter.graceplot.Tick(axis=None, onoff=True, major=None, minorticks=None, inout=None, majorsize=None, majorcolor=None, majorlinewidth=None, majorlinestyle=None, majorgrid=None, minorcolor=None, minorlinewidth=None, minorlinestyle=None, minorgrid=None, minorsize=None, placeon=None, type=None, default=None, TickLabel=None)

Bases: object

Controls appearence of ticks on an axis.

Parameters:

onoff

is either ‘on’ or ‘off’

major

is the space between ticks?

minorticks

is the number of minorticks between major ticks?

inout

determines if they point ‘in’ or ‘out’ or ‘both’

majorsize

determines how long the major ticks are

majorlinewidth

is how thick the major ticks are

majorlinestyle

is controls the linestle of the ticks and major gridlines

majorgrid

turns the major grid lines ‘on’ or ‘off’

minorcolor

is the color of the minor tick lines

minorlinewidth

minorlinestyle

controls the linestle of the ticks and minor gridlines

minorgrid

turns the minor gridlines on

minorsize

is the lengthe of the minor gridlines

placeon

is it is usually set to ‘both’,’normal’,’opposite’

type

is ? it is usually set to ‘auto’

default

is ? a number

output(axis)

list output to sent to grace

class jscatter.graceplot.TickLabel(axis=None, onoff=True, type=None, prec=None, format=None, append=None, prepend=None, angle=None, placeon=None, skip=None, stagger=None, op=None, sign=None, starttype=None, start=None, stoptype=None, stop=None, charsize=None, font=None, color=None)

Bases: object

Ticklabels

Parameters:

onoff‘on’,’off’

type ‘auto’

prec

format :string ,’general’ is default

decimal,exponential,general,power,scientific

appendstring

added to the end of the label

prependstring

added to the beginning of the label

anglefloat

degrees? of rotation

placeon‘normal’,’both’,’opposite’

where to place labels

skipint which skips some labels somehow

staggeris an integer that staggers the labels somehow

op‘bottom’ for x-axis, ‘left’ for y-axis

sign‘normal’

starttypestring ‘auto’

startfloat don;t know what it does

stoptypestring ‘auto’

stopfloat purpose?

charsizefloat for character size

fontinteger for the font

colorinteger for the color

Returns:

TickLabel object

output(axis)

list output to sent to grace

class jscatter.graceplot.createColorTable

Bases: object

assign(idx, rgb, name)

property len

property list

property names

class jscatter.graceplot.fills

Bases: object

none = 0

opaque = 8

solid = 1

class jscatter.graceplot.frames

Bases: object

breakbottom = 3

breakleft = 4

breakright = 5

breaktop = 2

closed = 0

halfopen = 1

jscatter.graceplot.inheritDocstringFrom(cls)

class jscatter.graceplot.lines

Bases: object

dashed = 3

dot_dashed = 5

dotted = 2

long_dashed = 4

none = 0

solid = 1

jscatter.graceplot.on_off(flag)

convert a bool into an xmgrace on/off string

class jscatter.graceplot.symbols

Bases: object

character = 11

circle = 1

cross = 9

diamond = 3

none = 0

plus = 8

square = 2

star = 10

triangle_down = 6

triangle_left = 5

triangle_right = 7

triangle_up = 4

jscatter.graceplot.test()