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adjusted fig 4 size and panels E and F

Paul Pfeiffer 3 years ago
parent
commit
1c44ce6f2d

+ 29 - 40
graphics/fig4.sla

@@ -1,6 +1,6 @@
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+ 664 - 5
scripts/spatial_network/perlin/figures.mplstyle

@@ -1,7 +1,666 @@
 
-font.size: 8
-axes.labelsize: medium
-xtick.labelsize: medium
-ytick.labelsize: medium
 
-savefig.dpi: 300
+#### TICKS
+## see http://matplotlib.org/api/axis_api.html#matplotlib.axis.Tick
+#xtick.top            : False  ## draw ticks on the top side
+#xtick.bottom         : True   ## draw ticks on the bottom side
+#xtick.labeltop       : False  ## draw label on the top
+#xtick.labelbottom    : True   ## draw label on the bottom
+#xtick.major.size     : 3.5    ## major tick size in points
+#xtick.minor.size     : 2      ## minor tick size in points
+#xtick.major.width    : 0.8    ## major tick width in points
+#xtick.minor.width    : 0.6    ## minor tick width in points
+xtick.major.pad      : 1.5    ## distance to major tick label in points
+xtick.minor.pad      : 1.4    ## distance to the minor tick label in points
+#xtick.color          : black  ## color of the tick labels
+#xtick.labelsize      : medium ## fontsize of the tick labels
+#xtick.direction      : out    ## direction: in, out, or inout
+#xtick.minor.visible  : False  ## visibility of minor ticks on x-axis
+#xtick.major.top      : True   ## draw x axis top major ticks
+#xtick.major.bottom   : True   ## draw x axis bottom major ticks
+#xtick.minor.top      : True   ## draw x axis top minor ticks
+#xtick.minor.bottom   : True   ## draw x axis bottom minor ticks
+#xtick.alignment      : center ## alignment of xticks
+
+#ytick.left           : True   ## draw ticks on the left side
+#ytick.right          : False  ## draw ticks on the right side
+#ytick.labelleft      : True   ## draw tick labels on the left side
+#ytick.labelright     : False  ## draw tick labels on the right side
+#ytick.major.size     : 3.5    ## major tick size in points
+#ytick.minor.size     : 2      ## minor tick size in points
+#ytick.major.width    : 0.8    ## major tick width in points
+#ytick.minor.width    : 0.6    ## minor tick width in points
+ytick.major.pad      : 1.5    ## distance to major tick label in points
+ytick.minor.pad      : 1.4    ## distance to the minor tick label in points
+#ytick.color          : black  ## color of the tick labels
+#ytick.labelsize      : medium ## fontsize of the tick labels
+#ytick.direction      : out    ## direction: in, out, or inout
+#ytick.minor.visible  : False  ## visibility of minor ticks on y-axis
+#ytick.major.left     : True   ## draw y axis left major ticks
+#ytick.major.right    : True   ## draw y axis right major ticks
+#ytick.minor.left     : True   ## draw y axis left minor ticks
+#ytick.minor.right    : True   ## draw y axis right minor ticks
+#ytick.alignment      : center_baseline ## alignment of yticks
+
+#### MATPLOTLIBRC FORMAT
+
+## This is a sample matplotlib configuration file - you can find a copy
+## of it on your system in
+## site-packages/matplotlib/mpl-data/matplotlibrc.  If you edit it
+## there, please note that it will be overwritten in your next install.
+## If you want to keep a permanent local copy that will not be
+## overwritten, place it in the following location:
+## unix/linux:
+##      $HOME/.config/matplotlib/matplotlibrc or
+##      $XDG_CONFIG_HOME/matplotlib/matplotlibrc (if $XDG_CONFIG_HOME is set)
+## other platforms:
+##      $HOME/.matplotlib/matplotlibrc
+##
+## See http://matplotlib.org/users/customizing.html#the-matplotlibrc-file for
+## more details on the paths which are checked for the configuration file.
+##
+## This file is best viewed in a editor which supports python mode
+## syntax highlighting. Blank lines, or lines starting with a comment
+## symbol, are ignored, as are trailing comments.  Other lines must
+## have the format
+##     key : val ## optional comment
+##
+## Colors: for the color values below, you can either use - a
+## matplotlib color string, such as r, k, or b - an rgb tuple, such as
+## (1.0, 0.5, 0.0) - a hex string, such as ff00ff - a scalar
+## grayscale intensity such as 0.75 - a legal html color name, e.g., red,
+## blue, darkslategray
+
+##### CONFIGURATION BEGINS HERE
+
+## The default backend. If you omit this parameter, the first
+## working backend from the following list is used:
+## MacOSX Qt5Agg Qt4Agg Gtk3Agg TkAgg WxAgg Agg
+##
+## Other choices include:
+## Qt5Cairo Qt4Cairo GTK3Cairo TkCairo WxCairo Cairo Wx PS PDF SVG Template.
+##
+## You can also deploy your own backend outside of matplotlib by
+## referring to the module name (which must be in the PYTHONPATH) as
+## 'module://my_backend'.
+#backend      : Agg
+
+## Note that this can be overridden by the environment variable
+## QT_API used by Enthought Tool Suite (ETS); valid values are
+## "pyqt" and "pyside".  The "pyqt" setting has the side effect of
+## forcing the use of Version 2 API for QString and QVariant.
+
+## The port to use for the web server in the WebAgg backend.
+#webagg.port : 8988
+
+## The address on which the WebAgg web server should be reachable
+#webagg.address : 127.0.0.1
+
+## If webagg.port is unavailable, a number of other random ports will
+## be tried until one that is available is found.
+#webagg.port_retries : 50
+
+## When True, open the webbrowser to the plot that is shown
+#webagg.open_in_browser : True
+
+## if you are running pyplot inside a GUI and your backend choice
+## conflicts, we will automatically try to find a compatible one for
+## you if backend_fallback is True
+#backend_fallback: True
+
+#interactive  : False
+#toolbar      : toolbar2   ## None | toolbar2  ("classic" is deprecated)
+#timezone     : UTC        ## a pytz timezone string, e.g., US/Central or Europe/Paris
+
+## Where your matplotlib data lives if you installed to a non-default
+## location.  This is where the matplotlib fonts, bitmaps, etc reside
+#datapath : /home/jdhunter/mpldata
+
+
+#### LINES
+## See http://matplotlib.org/api/artist_api.html#module-matplotlib.lines for more
+## information on line properties.
+#lines.linewidth   : 1.5     ## line width in points
+#lines.linestyle   : -       ## solid line
+#lines.color       : C0      ## has no affect on plot(); see axes.prop_cycle
+#lines.marker      : None    ## the default marker
+#lines.markerfacecolor  : auto    ## the default markerfacecolor
+#lines.markeredgecolor  : auto    ## the default markeredgecolor
+#lines.markeredgewidth  : 1.0     ## the line width around the marker symbol
+#lines.markersize  : 6            ## markersize, in points
+#lines.dash_joinstyle : round        ## miter|round|bevel
+#lines.dash_capstyle : butt          ## butt|round|projecting
+#lines.solid_joinstyle : round       ## miter|round|bevel
+#lines.solid_capstyle : projecting   ## butt|round|projecting
+#lines.antialiased : True         ## render lines in antialiased (no jaggies)
+
+## The three standard dash patterns.  These are scaled by the linewidth.
+#lines.dashed_pattern : 3.7, 1.6
+#lines.dashdot_pattern : 6.4, 1.6, 1, 1.6
+#lines.dotted_pattern : 1, 1.65
+#lines.scale_dashes : True
+
+#markers.fillstyle: full ## full|left|right|bottom|top|none
+
+#### PATCHES
+## Patches are graphical objects that fill 2D space, like polygons or
+## circles.  See
+## http://matplotlib.org/api/artist_api.html#module-matplotlib.patches
+## information on patch properties
+#patch.linewidth        : 1        ## edge width in points.
+#patch.facecolor        : C0
+#patch.edgecolor        : black   ## if forced, or patch is not filled
+#patch.force_edgecolor  : False   ## True to always use edgecolor
+#patch.antialiased      : True    ## render patches in antialiased (no jaggies)
+
+#### HATCHES
+#hatch.color     : black
+#hatch.linewidth : 1.0
+
+#### Boxplot
+#boxplot.notch       : False
+#boxplot.vertical    : True
+#boxplot.whiskers    : 1.5
+#boxplot.bootstrap   : None
+#boxplot.patchartist : False
+#boxplot.showmeans   : False
+#boxplot.showcaps    : True
+#boxplot.showbox     : True
+#boxplot.showfliers  : True
+#boxplot.meanline    : False
+
+#boxplot.flierprops.color           : black
+#boxplot.flierprops.marker          : o
+#boxplot.flierprops.markerfacecolor : none
+#boxplot.flierprops.markeredgecolor : black
+#boxplot.flierprops.markeredgewidth : 1.0
+#boxplot.flierprops.markersize      : 6
+#boxplot.flierprops.linestyle       : none
+#boxplot.flierprops.linewidth       : 1.0
+
+#boxplot.boxprops.color     : black
+#boxplot.boxprops.linewidth : 1.0
+#boxplot.boxprops.linestyle : -
+
+#boxplot.whiskerprops.color     : black
+#boxplot.whiskerprops.linewidth : 1.0
+#boxplot.whiskerprops.linestyle : -
+
+#boxplot.capprops.color     : black
+#boxplot.capprops.linewidth : 1.0
+#boxplot.capprops.linestyle : -
+
+#boxplot.medianprops.color     : C1
+#boxplot.medianprops.linewidth : 1.0
+#boxplot.medianprops.linestyle : -
+
+#boxplot.meanprops.color           : C2
+#boxplot.meanprops.marker          : ^
+#boxplot.meanprops.markerfacecolor : C2
+#boxplot.meanprops.markeredgecolor : C2
+#boxplot.meanprops.markersize      :  6
+#boxplot.meanprops.linestyle       : --
+#boxplot.meanprops.linewidth       : 1.0
+
+
+#### FONT
+
+## font properties used by text.Text.  See
+## http://matplotlib.org/api/font_manager_api.html for more
+## information on font properties.  The 6 font properties used for font
+## matching are given below with their default values.
+##
+## The font.family property has five values: 'serif' (e.g., Times),
+## 'sans-serif' (e.g., Helvetica), 'cursive' (e.g., Zapf-Chancery),
+## 'fantasy' (e.g., Western), and 'monospace' (e.g., Courier).  Each of
+## these font families has a default list of font names in decreasing
+## order of priority associated with them.  When text.usetex is False,
+## font.family may also be one or more concrete font names.
+##
+## The font.style property has three values: normal (or roman), italic
+## or oblique.  The oblique style will be used for italic, if it is not
+## present.
+##
+## The font.variant property has two values: normal or small-caps.  For
+## TrueType fonts, which are scalable fonts, small-caps is equivalent
+## to using a font size of 'smaller', or about 83%% of the current font
+## size.
+##
+## The font.weight property has effectively 13 values: normal, bold,
+## bolder, lighter, 100, 200, 300, ..., 900.  Normal is the same as
+## 400, and bold is 700.  bolder and lighter are relative values with
+## respect to the current weight.
+##
+## The font.stretch property has 11 values: ultra-condensed,
+## extra-condensed, condensed, semi-condensed, normal, semi-expanded,
+## expanded, extra-expanded, ultra-expanded, wider, and narrower.  This
+## property is not currently implemented.
+##
+## The font.size property is the default font size for text, given in pts.
+## 10 pt is the standard value.
+
+#font.family         : sans-serif
+#font.style          : normal
+#font.variant        : normal
+#font.weight         : normal
+#font.stretch        : normal
+## note that font.size controls default text sizes.  To configure
+## special text sizes tick labels, axes, labels, title, etc, see the rc
+## settings for axes and ticks. Special text sizes can be defined
+## relative to font.size, using the following values: xx-small, x-small,
+## small, medium, large, x-large, xx-large, larger, or smaller
+font.size           : 6.0
+#font.serif          : DejaVu Serif, Bitstream Vera Serif, Computer Modern Roman, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif
+#font.sans-serif     : DejaVu Sans, Bitstream Vera Sans, Computer Modern Sans Serif, Lucida Grande, Verdana, Geneva, Lucid, Arial, Helvetica, Avant Garde, sans-serif
+#font.cursive        : Apple Chancery, Textile, Zapf Chancery, Sand, Script MT, Felipa, cursive
+#font.fantasy        : Comic Sans MS, Chicago, Charcoal, ImpactWestern, Humor Sans, xkcd, fantasy
+#font.monospace      : DejaVu Sans Mono, Bitstream Vera Sans Mono, Computer Modern Typewriter, Andale Mono, Nimbus Mono L, Courier New, Courier, Fixed, Terminal, monospace
+
+#### TEXT
+## text properties used by text.Text.  See
+## http://matplotlib.org/api/artist_api.html#module-matplotlib.text for more
+## information on text properties
+#text.color          : black
+
+#### LaTeX customizations. See http://wiki.scipy.org/Cookbook/Matplotlib/UsingTex
+#text.usetex         : False  ## use latex for all text handling. The following fonts
+                              ## are supported through the usual rc parameter settings:
+                              ## new century schoolbook, bookman, times, palatino,
+                              ## zapf chancery, charter, serif, sans-serif, helvetica,
+                              ## avant garde, courier, monospace, computer modern roman,
+                              ## computer modern sans serif, computer modern typewriter
+                              ## If another font is desired which can loaded using the
+                              ## LaTeX \usepackage command, please inquire at the
+                              ## matplotlib mailing list
+#text.latex.preamble :      ## IMPROPER USE OF THIS FEATURE WILL LEAD TO LATEX FAILURES
+                            ## AND IS THEREFORE UNSUPPORTED. PLEASE DO NOT ASK FOR HELP
+                            ## IF THIS FEATURE DOES NOT DO WHAT YOU EXPECT IT TO.
+                            ## text.latex.preamble is a single line of LaTeX code that
+                            ## will be passed on to the LaTeX system. It may contain
+                            ## any code that is valid for the LaTeX "preamble", i.e.
+                            ## between the "\documentclass" and "\begin{document}"
+                            ## statements.
+                            ## Note that it has to be put on a single line, which may
+                            ## become quite long.
+                            ## The following packages are always loaded with usetex, so
+                            ## beware of package collisions: color, geometry, graphicx,
+                            ## type1cm, textcomp.
+                            ## Adobe Postscript (PSSNFS) font packages may also be
+                            ## loaded, depending on your font settings.
+#text.latex.preview : False
+
+#text.hinting : auto   ## May be one of the following:
+                       ##   none: Perform no hinting
+                       ##   auto: Use FreeType's autohinter
+                       ##   native: Use the hinting information in the
+                       #              font file, if available, and if your
+                       #              FreeType library supports it
+                       ##   either: Use the native hinting information,
+                       #              or the autohinter if none is available.
+                       ## For backward compatibility, this value may also be
+                       ## True === 'auto' or False === 'none'.
+#text.hinting_factor : 8 ## Specifies the amount of softness for hinting in the
+                         ## horizontal direction.  A value of 1 will hint to full
+                         ## pixels.  A value of 2 will hint to half pixels etc.
+#text.antialiased : True ## If True (default), the text will be antialiased.
+                         ## This only affects the Agg backend.
+
+## The following settings allow you to select the fonts in math mode.
+## They map from a TeX font name to a fontconfig font pattern.
+## These settings are only used if mathtext.fontset is 'custom'.
+## Note that this "custom" mode is unsupported and may go away in the
+## future.
+#mathtext.cal : cursive
+#mathtext.rm  : sans
+#mathtext.tt  : monospace
+#mathtext.it  : sans:italic
+#mathtext.bf  : sans:bold
+#mathtext.sf  : sans
+#mathtext.fontset : dejavusans ## Should be 'dejavusans' (default),
+                               ## 'dejavuserif', 'cm' (Computer Modern), 'stix',
+                               ## 'stixsans' or 'custom'
+#mathtext.fallback_to_cm : True  ## When True, use symbols from the Computer Modern
+                                 ## fonts when a symbol can not be found in one of
+                                 ## the custom math fonts.
+#mathtext.default : it ## The default font to use for math.
+                       ## Can be any of the LaTeX font names, including
+                       ## the special name "regular" for the same font
+                       ## used in regular text.
+
+#### AXES
+## default face and edge color, default tick sizes,
+## default fontsizes for ticklabels, and so on.  See
+## http://matplotlib.org/api/axes_api.html#module-matplotlib.axes
+#axes.facecolor      : white   ## axes background color
+#axes.edgecolor      : black   ## axes edge color
+#axes.linewidth      : 0.8     ## edge linewidth
+#axes.grid           : False   ## display grid or not
+#axes.grid.axis      : both    ## which axis the grid should apply to
+#axes.grid.which     : major   ## gridlines at major, minor or both ticks
+#axes.titlesize      : large   ## fontsize of the axes title
+#axes.titleweight    : normal  ## font weight of title
+#axes.titlepad       : 6.0     ## pad between axes and title in points
+#axes.labelsize      : medium  ## fontsize of the x any y labels
+axes.labelpad       : 1.5     ## space between label and axis
+#axes.labelweight    : normal  ## weight of the x and y labels
+#axes.labelcolor     : black
+#axes.axisbelow      : line    ## draw axis gridlines and ticks below
+                               ## patches (True); above patches but below
+                               ## lines ('line'); or above all (False)
+#axes.formatter.limits : -7, 7 ## use scientific notation if log10
+                               ## of the axis range is smaller than the
+                               ## first or larger than the second
+#axes.formatter.use_locale : False ## When True, format tick labels
+                                   ## according to the user's locale.
+                                   ## For example, use ',' as a decimal
+                                   ## separator in the fr_FR locale.
+#axes.formatter.use_mathtext : False ## When True, use mathtext for scientific
+                                     ## notation.
+#axes.formatter.min_exponent: 0 ## minimum exponent to format in scientific notation
+#axes.formatter.useoffset      : True    ## If True, the tick label formatter
+                                         ## will default to labeling ticks relative
+                                         ## to an offset when the data range is
+                                         ## small compared to the minimum absolute
+                                         ## value of the data.
+#axes.formatter.offset_threshold : 4     ## When useoffset is True, the offset
+                                         ## will be used when it can remove
+                                         ## at least this number of significant
+                                         ## digits from tick labels.
+#axes.spines.left   : True   ## display axis spines
+#axes.spines.bottom : True
+#axes.spines.top    : True
+#axes.spines.right  : True
+#axes.unicode_minus  : True    ## use unicode for the minus symbol
+                               ## rather than hyphen.  See
+                               ## http://en.wikipedia.org/wiki/Plus_and_minus_signs#Character_codes
+#axes.prop_cycle    : cycler('color', ['1f77b4', 'ff7f0e', '2ca02c', 'd62728', '9467bd', '8c564b', 'e377c2', '7f7f7f', 'bcbd22', '17becf'])
+                      ## color cycle for plot lines  as list of string
+                      ## colorspecs: single letter, long name, or web-style hex
+					  ## Note the use of string escapes here ('1f77b4', instead of 1f77b4)
+                      ## as opposed to the rest of this file.
+#axes.autolimit_mode : data ## How to scale axes limits to the data.
+                            ## Use "data" to use data limits, plus some margin
+                            ## Use "round_number" move to the nearest "round" number
+#axes.xmargin        : .05  ## x margin.  See `axes.Axes.margins`
+#axes.ymargin        : .05  ## y margin See `axes.Axes.margins`
+#polaraxes.grid      : True    ## display grid on polar axes
+#axes3d.grid         : True    ## display grid on 3d axes
+
+#### DATES
+## These control the default format strings used in AutoDateFormatter.
+## Any valid format datetime format string can be used (see the python
+## `datetime` for details).  For example using '%%x' will use the locale date representation
+## '%%X' will use the locale time representation and '%%c' will use the full locale datetime
+## representation.
+## These values map to the scales:
+##     {'year': 365, 'month': 30, 'day': 1, 'hour': 1/24, 'minute': 1 / (24 * 60)}
+
+#date.autoformatter.year     : %Y
+#date.autoformatter.month    : %Y-%m
+#date.autoformatter.day      : %Y-%m-%d
+#date.autoformatter.hour     : %m-%d %H
+#date.autoformatter.minute   : %d %H:%M
+#date.autoformatter.second   : %H:%M:%S
+#date.autoformatter.microsecond   : %M:%S.%f
+
+#### TICKS
+## see http://matplotlib.org/api/axis_api.html#matplotlib.axis.Tick
+#xtick.top            : False  ## draw ticks on the top side
+#xtick.bottom         : True   ## draw ticks on the bottom side
+#xtick.labeltop       : False  ## draw label on the top
+#xtick.labelbottom    : True   ## draw label on the bottom
+#xtick.major.size     : 3.5    ## major tick size in points
+#xtick.minor.size     : 2      ## minor tick size in points
+#xtick.major.width    : 0.8    ## major tick width in points
+#xtick.minor.width    : 0.6    ## minor tick width in points
+xtick.major.pad      : 1.5    ## distance to major tick label in points
+xtick.minor.pad      : 1.4    ## distance to the minor tick label in points
+#xtick.color          : black  ## color of the tick labels
+#xtick.labelsize      : medium ## fontsize of the tick labels
+#xtick.direction      : out    ## direction: in, out, or inout
+#xtick.minor.visible  : False  ## visibility of minor ticks on x-axis
+#xtick.major.top      : True   ## draw x axis top major ticks
+#xtick.major.bottom   : True   ## draw x axis bottom major ticks
+#xtick.minor.top      : True   ## draw x axis top minor ticks
+#xtick.minor.bottom   : True   ## draw x axis bottom minor ticks
+#xtick.alignment      : center ## alignment of xticks
+
+#ytick.left           : True   ## draw ticks on the left side
+#ytick.right          : False  ## draw ticks on the right side
+#ytick.labelleft      : True   ## draw tick labels on the left side
+#ytick.labelright     : False  ## draw tick labels on the right side
+#ytick.major.size     : 3.5    ## major tick size in points
+#ytick.minor.size     : 2      ## minor tick size in points
+#ytick.major.width    : 0.8    ## major tick width in points
+#ytick.minor.width    : 0.6    ## minor tick width in points
+ytick.major.pad      : 1.5    ## distance to major tick label in points
+ytick.minor.pad      : 1.4    ## distance to the minor tick label in points
+#ytick.color          : black  ## color of the tick labels
+#ytick.labelsize      : medium ## fontsize of the tick labels
+#ytick.direction      : out    ## direction: in, out, or inout
+#ytick.minor.visible  : False  ## visibility of minor ticks on y-axis
+#ytick.major.left     : True   ## draw y axis left major ticks
+#ytick.major.right    : True   ## draw y axis right major ticks
+#ytick.minor.left     : True   ## draw y axis left minor ticks
+#ytick.minor.right    : True   ## draw y axis right minor ticks
+#ytick.alignment      : center_baseline ## alignment of yticks
+
+#### GRIDS
+#grid.color       :   b0b0b0    ## grid color
+#grid.linestyle   :   -         ## solid
+#grid.linewidth   :   0.8       ## in points
+#grid.alpha       :   1.0       ## transparency, between 0.0 and 1.0
+
+#### Legend
+#legend.loc           : best
+#legend.frameon       : True     ## if True, draw the legend on a background patch
+#legend.framealpha    : 0.8      ## legend patch transparency
+#legend.facecolor     : inherit  ## inherit from axes.facecolor; or color spec
+#legend.edgecolor     : 0.8      ## background patch boundary color
+#legend.fancybox      : True     ## if True, use a rounded box for the
+                                 ## legend background, else a rectangle
+#legend.shadow        : False    ## if True, give background a shadow effect
+#legend.numpoints     : 1        ## the number of marker points in the legend line
+#legend.scatterpoints : 1        ## number of scatter points
+#legend.markerscale   : 1.0      ## the relative size of legend markers vs. original
+#legend.fontsize      : medium
+#legend.title_fontsize    : None ## None sets to the same as the default axes.
+## Dimensions as fraction of fontsize:
+#legend.borderpad     : 0.4      ## border whitespace
+#legend.labelspacing  : 0.5      ## the vertical space between the legend entries
+#legend.handlelength  : 2.0      ## the length of the legend lines
+#legend.handleheight  : 0.7      ## the height of the legend handle
+#legend.handletextpad : 0.8      ## the space between the legend line and legend text
+#legend.borderaxespad : 0.5      ## the border between the axes and legend edge
+#legend.columnspacing : 2.0      ## column separation
+
+#### FIGURE
+## See http://matplotlib.org/api/figure_api.html#matplotlib.figure.Figure
+#figure.titlesize : large      ## size of the figure title (Figure.suptitle())
+#figure.titleweight : normal   ## weight of the figure title
+#figure.figsize   : 6.4, 4.8   ## figure size in inches
+#figure.dpi       : 100        ## figure dots per inch
+#figure.facecolor : white      ## figure facecolor
+#figure.edgecolor : white      ## figure edgecolor
+#figure.frameon : True         ## enable figure frame
+#figure.max_open_warning : 20  ## The maximum number of figures to open through
+                               ## the pyplot interface before emitting a warning.
+                               ## If less than one this feature is disabled.
+## The figure subplot parameters.  All dimensions are a fraction of the
+#figure.subplot.left    : 0.125  ## the left side of the subplots of the figure
+#figure.subplot.right   : 0.9    ## the right side of the subplots of the figure
+#figure.subplot.bottom  : 0.11   ## the bottom of the subplots of the figure
+#figure.subplot.top     : 0.88   ## the top of the subplots of the figure
+#figure.subplot.wspace  : 0.2    ## the amount of width reserved for space between subplots,
+                                 ## expressed as a fraction of the average axis width
+#figure.subplot.hspace  : 0.2    ## the amount of height reserved for space between subplots,
+                                 ## expressed as a fraction of the average axis height
+
+## Figure layout
+#figure.autolayout : False     ## When True, automatically adjust subplot
+                               ## parameters to make the plot fit the figure
+                               ## using `tight_layout`
+#figure.constrained_layout.use: False ## When True, automatically make plot
+                                      ## elements fit on the figure. (Not compatible
+                                      ## with `autolayout`, above).
+#figure.constrained_layout.h_pad : 0.04167 ## Padding around axes objects. Float representing
+#figure.constrained_layout.w_pad : 0.04167 ##  inches. Default is 3./72. inches (3 pts)
+#figure.constrained_layout.hspace : 0.02   ## Space between subplot groups. Float representing
+#figure.constrained_layout.wspace : 0.02   ##  a fraction of the subplot widths being separated.
+
+#### IMAGES
+#image.aspect : equal             ## equal | auto | a number
+#image.interpolation  : nearest   ## see help(imshow) for options
+#image.cmap   : viridis           ## A colormap name, gray etc...
+#image.lut    : 256               ## the size of the colormap lookup table
+#image.origin : upper             ## lower | upper
+#image.resample  : True
+#image.composite_image : True     ## When True, all the images on a set of axes are
+                                  ## combined into a single composite image before
+                                  ## saving a figure as a vector graphics file,
+                                  ## such as a PDF.
+
+#### CONTOUR PLOTS
+#contour.negative_linestyle : dashed ## string or on-off ink sequence
+#contour.corner_mask        : True   ## True | False | legacy
+
+#### ERRORBAR PLOTS
+#errorbar.capsize : 0             ## length of end cap on error bars in pixels
+
+#### HISTOGRAM PLOTS
+#hist.bins : 10                   ## The default number of histogram bins.
+                                  ## If Numpy 1.11 or later is
+                                  ## installed, may also be `auto`
+
+#### SCATTER PLOTS
+#scatter.marker : o               ## The default marker type for scatter plots.
+#scatter.edgecolors : face        ## The default edgecolors for scatter plots.
+
+#### Agg rendering
+#### Warning: experimental, 2008/10/10
+#agg.path.chunksize : 0           ## 0 to disable; values in the range
+                                  ## 10000 to 100000 can improve speed slightly
+                                  ## and prevent an Agg rendering failure
+                                  ## when plotting very large data sets,
+                                  ## especially if they are very gappy.
+                                  ## It may cause minor artifacts, though.
+                                  ## A value of 20000 is probably a good
+                                  ## starting point.
+#### PATHS
+#path.simplify : True   ## When True, simplify paths by removing "invisible"
+                        ## points to reduce file size and increase rendering
+                        ## speed
+#path.simplify_threshold : 0.111111111111  ## The threshold of similarity below which
+                                           ## vertices will be removed in the
+                                           ## simplification process
+#path.snap : True ## When True, rectilinear axis-aligned paths will be snapped to
+                  ## the nearest pixel when certain criteria are met.  When False,
+                  ## paths will never be snapped.
+#path.sketch : None ## May be none, or a 3-tuple of the form (scale, length,
+                    ## randomness).
+                    ## *scale* is the amplitude of the wiggle
+                    ## perpendicular to the line (in pixels).  *length*
+                    ## is the length of the wiggle along the line (in
+                    ## pixels).  *randomness* is the factor by which
+                    ## the length is randomly scaled.
+#path.effects : []  ##
+
+#### SAVING FIGURES
+## the default savefig params can be different from the display params
+## e.g., you may want a higher resolution, or to make the figure
+## background white
+savefig.dpi          : 300   ## figure dots per inch or 'figure'
+#savefig.facecolor   : white    ## figure facecolor when saving
+#savefig.edgecolor   : white    ## figure edgecolor when saving
+#savefig.format      : png      ## png, ps, pdf, svg
+#savefig.bbox        : standard ## 'tight' or 'standard'.
+                                ## 'tight' is incompatible with pipe-based animation
+                                ## backends but will workd with temporary file based ones:
+                                ## e.g. setting animation.writer to ffmpeg will not work,
+                                ## use ffmpeg_file instead
+#savefig.pad_inches  : 0.1      ## Padding to be used when bbox is set to 'tight'
+#savefig.jpeg_quality: 95       ## when a jpeg is saved, the default quality parameter.
+#savefig.directory   : ~        ## default directory in savefig dialog box,
+                                ## leave empty to always use current working directory
+#savefig.transparent : False    ## setting that controls whether figures are saved with a
+                                ## transparent background by default
+#savefig.orientation : portrait	## Orientation of saved figure
+
+### tk backend params
+#tk.window_focus   : False    ## Maintain shell focus for TkAgg
+
+### ps backend params
+#ps.papersize      : letter   ## auto, letter, legal, ledger, A0-A10, B0-B10
+#ps.useafm         : False    ## use of afm fonts, results in small files
+#ps.usedistiller   : False    ## can be: None, ghostscript or xpdf
+                                          ## Experimental: may produce smaller files.
+                                          ## xpdf intended for production of publication quality files,
+                                          ## but requires ghostscript, xpdf and ps2eps
+#ps.distiller.res  : 6000      ## dpi
+#ps.fonttype       : 3         ## Output Type 3 (Type3) or Type 42 (TrueType)
+
+### pdf backend params
+#pdf.compression   : 6   ## integer from 0 to 9
+                         ## 0 disables compression (good for debugging)
+#pdf.fonttype       : 3         ## Output Type 3 (Type3) or Type 42 (TrueType)
+#pdf.use14corefonts : False
+#pdf.inheritcolor : False
+
+### svg backend params
+#svg.image_inline : True       ## write raster image data directly into the svg file
+#svg.fonttype :   path         ## How to handle SVG fonts:
+   ##     none: Assume fonts are installed on the machine where the SVG will be viewed.
+   ##     path: Embed characters as paths -- supported by most SVG renderers
+#svg.hashsalt : None           ## if not None, use this string as hash salt
+                               ## instead of uuid4
+### pgf parameter
+#pgf.rcfonts : True
+#pgf.preamble :            ## see text.latex.preamble for documentation
+#pgf.texsystem : xelatex
+
+### docstring params
+##docstring.hardcopy = False  ## set this when you want to generate hardcopy docstring
+
+## Event keys to interact with figures/plots via keyboard.
+## Customize these settings according to your needs.
+## Leave the field(s) empty if you don't need a key-map. (i.e., fullscreen : '')
+#keymap.fullscreen : f, ctrl+f       ## toggling
+#keymap.home : h, r, home            ## home or reset mnemonic
+#keymap.back : left, c, backspace, MouseButton.BACK  ## forward / backward keys
+#keymap.forward : right, v, MouseButton.FORWARD      ## for quick navigation
+#keymap.pan : p                      ## pan mnemonic
+#keymap.zoom : o                     ## zoom mnemonic
+#keymap.save : s, ctrl+s             ## saving current figure
+#keymap.help : f1                    ## display help about active tools
+#keymap.quit : ctrl+w, cmd+w, q      ## close the current figure
+#keymap.quit_all : W, cmd+W, Q       ## close all figures
+#keymap.grid : g                     ## switching on/off major grids in current axes
+#keymap.grid_minor : G               ## switching on/off minor grids in current axes
+#keymap.yscale : l                   ## toggle scaling of y-axes ('log'/'linear')
+#keymap.xscale : k, L                ## toggle scaling of x-axes ('log'/'linear')
+#keymap.all_axes : a                 ## enable all axes
+#keymap.copy : ctrl+c, cmd+c         ## Copy figure to clipboard
+
+###ANIMATION settings
+#animation.html :  none            ## How to display the animation as HTML in
+                                   ## the IPython notebook. 'html5' uses
+                                   ## HTML5 video tag; 'jshtml' creates a
+                                   ## Javascript animation
+#animation.writer : ffmpeg         ## MovieWriter 'backend' to use
+#animation.codec : h264            ## Codec to use for writing movie
+#animation.bitrate: -1             ## Controls size/quality tradeoff for movie.
+                                   ## -1 implies let utility auto-determine
+#animation.frame_format:  png      ## Controls frame format used by temp files
+#animation.html_args:              ## Additional arguments to pass to html writer
+#animation.ffmpeg_path:  ffmpeg    ## Path to ffmpeg binary. Without full path
+                                   ## $PATH is searched
+#animation.ffmpeg_args:            ## Additional arguments to pass to ffmpeg
+#animation.avconv_path:  avconv    ## Path to avconv binary. Without full path
+                                   ## $PATH is searched
+#animation.avconv_args:            ## Additional arguments to pass to avconv
+#animation.convert_path:  convert  ## Path to ImageMagick's convert binary.
+                                   ## On Windows use the full path since convert
+                                   ## is also the name of a system tool.
+#animation.convert_args:           ## Additional arguments to pass to convert
+#animation.embed_limit : 20.0      ## Limit, in MB, of size of base64 encoded
+                                   ## animation in HTML (i.e. IPython notebook)

+ 31 - 9
scripts/spatial_network/perlin/paper_figures_spatial_head_direction_network_perlin_map.py

@@ -1,3 +1,4 @@
+import logging
 import os
 
 import matplotlib.legend as mlegend
@@ -14,15 +15,16 @@ from pypet.brian2 import Brian2MonitorResult
 from scripts.interneuron_placement import get_position_mesh, Pickle, get_correct_position_mesh
 from scripts.spatial_network.figures_spatial_head_direction_network_orientation_map import plot_hdi_in_space
 from scripts.spatial_network.perlin.figure_utils import remove_frame, remove_ticks, add_length_scale
-from scripts.spatial_network.perlin.run_entropy_maximisation_perlin_map import DATA_FOLDER, TRAJ_NAME
+from scripts.spatial_network.perlin.run_entropy_maximisation_perlin_map import DATA_FOLDER, TRAJ_NAME, \
+    get_input_head_directions
 
 plt.style.use('figures.mplstyle')
 
 FIGURE_SAVE_PATH = '../../../figures/figure_4_paper_perlin/'
 # FIGURE_SAVE_PATH = '../../figures/figure_4_poster_fens/'
 cm_per_inch = 2.54
-number_of_panels = 5.0
-page_size = 16.0
+number_of_panels = 4.0
+page_size = 11.4
 panel_size = page_size / number_of_panels / cm_per_inch
 print(panel_size)
 
@@ -946,7 +948,7 @@ def plot_hdi_histogram_combined_and_overlayed(traj, plot_run_names, ex_polar_plo
     # print(gs.get_subplot_params())
 
     width = 2 * panel_size
-    height = 1.5 * panel_size
+    height = 1.2 * panel_size
     fig, axes = plt.subplots(2, 1, figsize=(width, height))
     plt.subplots_adjust(wspace=0, hspace=0.1)
     bins = np.linspace(0.0, 1.0, 21, endpoint=True)
@@ -1063,7 +1065,6 @@ def filter_run_names_by_par_dict(traj, par_dict):
 
     return run_name_list
 
-
 def plot_exc_and_inh_hdi_over_corr_len(traj, plot_run_names):
     corr_len_expl = traj.f_get('correlation_length').f_get_range()
     seed_expl = traj.f_get('seed').f_get_range()
@@ -1110,7 +1111,7 @@ def plot_exc_and_inh_hdi_over_corr_len(traj, plot_run_names):
     # markers = [verts, '', 'o']
 
     width = 2*panel_size
-    height = 1.5*panel_size
+    height = 1.2*panel_size
     fig, ax = plt.subplots(1, 1, figsize=(width, height))
 
     for label in sorted(label_range, reverse=True):
@@ -1132,6 +1133,9 @@ def plot_exc_and_inh_hdi_over_corr_len(traj, plot_run_names):
         inh_hdi_std = inh_hdi_n_and_seed_std_dev[:, label]
 
         corr_len_range = exc_hdi_mean.keys().to_numpy()
+        print(label)
+        for corr_len, ex_hdi, in_hdi in zip(corr_len_range, exc_hdi_mean, inh_hdi_mean):
+            print("length: {:.2f} um, ex hdi: {:.2f} and in hdi {:.2f}".format(corr_len, ex_hdi, in_hdi))
 
         exc_col, exc_lin, exc_mar, exc_mar_size = exc_style_dict[label]
         inh_col, inh_lin, inh_mar, inh_mar_size = inh_style_dict[label]
@@ -1351,13 +1355,31 @@ if __name__ == "__main__":
     traj.v_auto_load = True
     save_figs = True
 
-    plot_corr_len = get_closest_correlation_length(traj, 200.0)
-    par_dict = {'seed': 1, 'correlation_length': plot_corr_len}
+    print("# Plotting script polarized interneurons")
+
+    map_length_scale = 200.0
+    map_seed = 1
+    exemplary_head_direction = 0
+
+    print("## Map specifications")
+    print("\tcorrelation length: {:.1f} um".format(map_length_scale))
+    print("\tmap seed: {:d}".format(map_seed))
+
+    print("## Input specification")
+    print("\tselected head direction: {:.0f}°".format(exemplary_head_direction))
+    plot_corr_len = get_closest_correlation_length(traj, map_length_scale)
+    par_dict = {'seed': map_seed, 'correlation_length': plot_corr_len}
+
+    print("## Figure specification")
+    print("\tpanel size: {:.2f} cm".format(panel_size*cm_per_inch))
+
     plot_run_names = filter_run_names_by_par_dict(traj, par_dict)
     print(traj.map.sheet_size)
     print(plot_run_names)
 
-    direction_idx = 6
+
+    directions = get_input_head_directions(traj)
+    direction_idx = np.argmin(np.abs(np.array(directions)-np.deg2rad(exemplary_head_direction)))
 
     selected_neuron_excitatory = 1716
     selected_inhibitory_neuron = 144

+ 6 - 1
scripts/spatial_network/perlin/run_entropy_maximisation_perlin_map.py

@@ -88,7 +88,7 @@ def spatial_network_with_entropy_maximisation(traj):
 
     sharpness = 1.0 / (traj.input.width) ** 2
 
-    directions = np.linspace(-np.pi, np.pi, traj.input.number_of_directions, endpoint=False)
+    directions = get_input_head_directions(traj)
     for idx, dir in enumerate(directions):
         # We recreate the network here for every dir, which slows down the simulation quite considerably. Otherwise,
         # we get a problem with saving and restoring the spike times (0s spike for neuron 0)
@@ -136,6 +136,11 @@ def spatial_network_with_entropy_maximisation(traj):
     return 1
 
 
+def get_input_head_directions(traj):
+    directions = np.linspace(-np.pi, np.pi, traj.input.number_of_directions, endpoint=False)
+    return directions
+
+
 def main():
     env = Environment(trajectory=TRAJ_NAME,
                       comment="Compare the head direction tuning for circular and ellipsoid interneuron morphology, "