Pyadmin: 1 revision

2014-03-28T01:53:13Z

1 revision

MartinChristen: New script to easily create figures. ~~~~

2013-02-13T16:56:46Z

New script to easily create figures. ~~~~

New page

= Overview =
This script will aid you in making publication quality figures for the currently displayed scene.
It understands a variety of preset "modes" and sizes.

= Usage =
<source lang="python">
make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]
</source>

The parameters are:

'''filename''' : The name of the resulting image file.
::''The extension '''.png''' is added automatically.''

''NOTE'': if no further arguments are given, the script generates quick figures for general use:
::* figures are not ray-traced
::* TWO figures at 300 x 300 px, 72 dpi
::* views are rotated 180° about y (front and back view)
::* _front_quick and _back_quick are appended to the filename

'''mode''' : Type of figure desired. Possible values are as follows:

::'''''single''''' = "single view"
::* one ray-traced 300 dpi figure of the current view

::'''''fb''''' = "front and back view"
::* TWO ray-traced 300 dpi figures
::* views are rotated 180° about y
::* _front and _back are appended to the filename

::'''''sides''''' = "four side views"
::* FOUR ray-traced 300 dpi figures
::* view is incrementally rotated by 90° about y
::* _1, _2, _3, and _4 are appended to the filename

::'''''stereo''''' = "stereoview"
::* TWO ray-traced 300 dpi figures
::* views are shifted by +/- 3 degrees
::* image dimensions are fixed at 750 x 750 pixels (size arguments are ignored)
::* _L and _R are appended to the filename
::* the output files are meant to be combined side by side to generate a stereo image

'''size''' : Size of the figure(s) in pixels or in "panels"
::* DEFAULT = 900 pixels if a mode is specified
::* if size is 12 or smaller, the script interprets it as a number of "panels" to make.
::* panel sizes in pixels are hardcoded in the source but can easily be modified.

'''opaque''' : Create an opaque background.
::* By default the figure background is 100% transparent.

= Examples =
<source lang="python">

#quick 'n' dirty front and back views of the scene
#300x300 pixels at 72 dpi, transparent background
# filenames will be output_front_quick.png and output_back_quick.png
make_figure output

# one ray-traced PNG file 975x975 pixels at 300dpi, with opaque background
# filename will be output.png
make_figure output, single, 975, opaque

# two panels (1350x1350 px each at 300dpi) of the "front" and "back" view on transparent background
# filenames will be output_front.png and output_back.png
make_figure output, fb, 2

# four panels (900x900 px each) where the view is incrementally rotated by 90° about y, transparent background
# filenames will be output_1.png, output_2.png, output_3.png and output_4.png
make_figure output, sides,4

#stereoview of the current scene with opaque background
#size is fixed to 2x 750x750px
# filenames will be output_L.png and output_R.png
make_figure output, stereo, opaque
</source>

= The Code =
<source lang="python">
#make_figure v.3.0
#Copyleft Martin Christen, 2010

from pymol import cmd
def make_figure(output='', mode='',size=900,opaque='transparent'):

"""

AUTHOR

Martin Christen

DESCRIPTION

"make_figure" creates publication-quality figures of the current scene.
It understands several predefined "modes" and sizes.

USAGE

make_figure filename [, mode] [, size (default=900 pixels)] [,opaque]

ARGUMENTS

mode = string: type of desired figure (single, fb, sides, stereo or -nothing-)
size = integer: size of the figure in pixels OR # panels (if <= 12)
opaque = specify an opaque background.
By default, the script makes the background transparent.
EXAMPLES

make_figure output
make_figure output, single, 975, opaque
make_figure output, fb, 2
make_figure output, sides,4
make_figure output, stereo

NOTES

"single" mode makes a single 300 dpi figure

"fb" mode makes TWO 300 dpi figure
("front" and "back", rotating by 180 degrees about y)

"sides" mode makes FOUR 300 dpi figures
("front" "left" "right" and back, rotating by 90 degrees clockwise about y)

"stereo" generates two 300 dpi, 750 px figures
("L" and "R", to be combined as a stereo image)
If you specify the stereo mode, the size argument is IGNORED.

If no mode argument is given, the script generates quick figures
for general use: TWO figures (front and back) at 300 x 300 px, 72 dpi.

Size is interpreted as pixels, except if the number is ridiculously small
(<=12), in which case the script as "number of panels" to make.

Edit the script manually to define corresponding values.

"""

#define sizes here (in pixels)
panel1 = 1800
panel2 = 1350
panel3 = 900
panel4 = 900
panel5 = 750
panel6 = 750
panel7 = 675
panel8 = 675
panel9 = 600
panel10 = 585
panel11 = 585
panel12 = 585

#verify size is an integer number and convert to pixels
size = int(size)
if size > 12:
pixels = size

elif size == 1:
pixels = panel1

elif size == 2:
pixels = panel2

elif size == 3:
pixels = panel3

elif size == 4:
pixels = panel4

elif size == 5:
pixels = panel5

elif size == 6:
pixels = panel6

elif size == 7:
pixels = panel7

elif size == 8:
pixels = panel8

elif size == 9:
pixels = panel9

elif size == 10:
pixels = panel10

elif size == 11:
pixels = panel11

elif size == 3:
pixels = panel12

#change background
cmd.unset('opaque_background')
if opaque == 'opaque':
cmd.set('opaque_background')

#apply mode
if output == '':
print 'no output filename defined\n'
print 'try: \'make_figure filename\''
return -1
# abort if no output file name given

if mode =='':
cmd.set('surface_quality',1)
cmd.set('opaque_background')
cmd.png(output+"_back_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.png(output+"_front_quick",300,300,dpi=72)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for quick mode

elif mode == 'single':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output, dpi=300)
cmd.set('surface_quality',0)
# make a figure for single mode

elif mode == 'fb':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_front", dpi=300)
cmd.turn('y',180)
cmd.ray(pixels, pixels)
cmd.png(output+"_back", dpi=300)
cmd.turn('y',180)
cmd.set('surface_quality',0)
# make front and back figures for single mode

elif mode == 'sides':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(pixels, pixels)
cmd.png(output+"_1", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_2", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_3", dpi=300)
cmd.turn('y',90)
cmd.ray(pixels, pixels)
cmd.png(output+"_4", dpi=300)
cmd.turn('y',90)
cmd.set('surface_quality',0)
# make front and back figures for single mode

elif mode == 'stereo':
cmd.set('surface_quality',1)
cmd.set('ray_shadow',0)
cmd.ray(750, 750, angle=-3)
cmd.png(output+"_R", dpi=300)
cmd.ray(750, 750, angle=3)
cmd.png(output+"_L", dpi=300)
# make stereo figure (for more control use stereo_ray)

cmd.extend('make_figure',make_figure)
</source>

[[Category:Script_Library]]
[[Category:UI_Scripts]]

← Older revision	Revision as of 01:53, 28 March 2014
(No difference)

Make Figures - Revision history

Pyadmin: 1 revision

MartinChristen: New script to easily create figures. ~~~~