I'm trying to use the answers I found in these questions:
How to save a plot into a PDF file without a large margin around
Get rid of the white space around matlab figure's pdf output
External source
to print a matlab plot to pdf without having the white margins included.
However using this code:
function saveTightFigure( h, outfilename, orientation )
% SAVETIGHTFIGURE(H,OUTFILENAME) Saves figure H in file OUTFILENAME without
% the white space around it.
%
% by ``a grad student"
% http://tipstrickshowtos.blogspot.com/2010/08/how-to-get-rid-of-white-margin-in.html
% get the current axes
ax = get(h, 'CurrentAxes');
% make it tight
ti = get(ax,'TightInset');
set(ax,'Position',[ti(1) ti(2) 1-ti(3)-ti(1) 1-ti(4)-ti(2)]);
% adjust the papersize
set(ax,'units','centimeters');
pos = get(ax,'Position');
ti = get(ax,'TightInset');
set(h, 'PaperUnits','centimeters');
set(h, 'PaperSize', [pos(3)+ti(1)+ti(3) pos(4)+ti(2)+ti(4)]);
set(h, 'PaperPositionMode', 'manual');
set(h, 'PaperPosition',[0 0 pos(3)+ti(1)+ti(3) pos(4)+ti(2)+ti(4)]);
% save it
%saveas(h,outfilename);
if( orientation == 1)
orient portrait
else
orient landscape
end
print( '-dpdf', outfilename );
end
Results in this output:
As you can see the 'PaperSize' seems to be set not properly. Any idea of possible fixes?
NOTE
If I change the orientation between landscape and portrait the result is the same, simply the image is chopped in a different way.
However if I save the image with the saveas(h,outfilename); instruction the correct output is produced.
Why is this? And what is the difference between the two saving instructions?
Alltogether the answers you mentioned offer a lot of approaches, but most of them didn't worked for me neither. Most of them screw up your papersize when you want to get the tight inset, the only which worked for me was:
set(axes_handle,'LooseInset',get(axes_handle,'TightInset'));
I finally wrote a function, where I specify the exact height and width of the output figure on paper, and the margin I want (or just set it to zero). Be aware that you also need to pass the axis handle. Maybe this functions works for you also.
function saveFigure( fig_handle, axes_handle, name , height , width , margin)
set(axes_handle,'LooseInset',get(axes_handle,'TightInset'));
set(fig_handle, 'Units','centimeters','PaperUnits','centimeters')
% the last two parameters of 'Position' define the figure size
set(fig_handle,'Position',[-margin -margin width height],...
'PaperPosition',[0 0 width+margin height+margin],...
'PaperSize',[width+margin height+margin],...
'PaperPositionMode','auto',...
'InvertHardcopy', 'on',...
'Renderer','painters'... %recommended if there are no alphamaps
);
saveas(fig_handle,name,'pdf')
end
Edit: if you use painters as renderer saveas and print should produce similar results. For jpegs print is preferable as you can specify the resolution.
Related
I am trying to use gnuplot 5.0 to plot a 2D array of data with no margins or borders or axes... just a 2D image (.png or .jpg) representing some data. I would like to have each array element to correspond to exactly one pixel in the image with no scaling / interpolation etc and no extra white pixels at the edges.
So far, when I try to set the margins to 0 and even using the pixels flag, I am still left with a row of white pixels on the right and top borders of the image.
How can I get just an image file with pixel-by-pixel representation of a data array and nothing extra?
gnuplot script:
#!/usr/bin/gnuplot --persist
set terminal png size 400, 200
set size ratio -1
set lmargin at screen 0
set rmargin at screen 1
set tmargin at screen 0
set bmargin at screen 1
unset colorbox
unset tics
unset xtics
unset ytics
unset border
unset key
set output "pic.png"
plot "T.dat" binary array=400x200 format="%f" with image pixels notitle
Example data from Fortran 90:
program main
implicit none
integer, parameter :: nx = 400
integer, parameter :: ny = 200
real, dimension (:,:), allocatable :: T
allocate (T(nx,ny))
T(:,:)=0.500
T(2,2)=5.
T(nx-1,ny-1)=5.
T(2,ny-1)=5.
T(nx-1,2)=5.
open(3, file="T.dat", access="stream")
write(3) T(:,:)
close(3)
end program main
Some gnuplot terminals implement "with image" by creating a separate png file containing the image and then linking to it inside the resulting plot. Using that separate png image file directly will avoid any issues of page layout, margins, etc. Here I use the canvas terminal. The plot itself is thrown away; all we keep is the png file created with the desired content.
gnuplot> set term canvas name 'myplot'
Terminal type is now 'canvas'
Options are ' rounded size 600,400 enhanced fsize 10 lw 1 fontscale 1 standalone'
gnuplot> set output '/dev/null'
gnuplot> plot "T.dat" binary array=400x200 format="%f" with image
linking image 1 to external file myplot_image_01.png
gnuplot> quit
$identify myplot_image_01.png
myplot_image_01.png PNG 400x200 400x200+0+0 8-bit sRGB 348B 0.000u 0:00.000
Don't use gnuplot.
Instead, write a script that reads your data and converts it into one of the Portable Anymap formats. Here's an example in Python:
#!/usr/bin/env python3
import math
import struct
width = 400
height = 200
levels = 255
raw_datum_fmt = '=d' # native, binary double-precision float
raw_datum_size = struct.calcsize(raw_datum_fmt)
with open('T.dat', 'rb') as f:
print("P2")
print("{} {}".format(width, height))
print("{}".format(levels))
raw_data = f.read(width * height * raw_datum_size)
for y in range(height):
for x in range(width):
raw_datum, = struct.unpack_from(raw_datum_fmt, raw_data, (y * width + x) * raw_datum_size)
datum = math.floor(raw_datum * levels) # assume a number in the range [0, 1]
print("{:>3} ".format(datum), end='')
print()
If you can modify the program which generates the data file, you can even skip the above step and instead generate the data directly in a PNM format.
Either way, you can then use ImageMagick to convert the image to a format of your choice:
./convert.py | convert - pic.png
This should be an easy task, however, apparently it's not.
The following might be a (cumbersome) solution because all other attempts failed. My suspicion is that some graphics library has an issue which you probably cannot solve as a gnuplot user.
You mentioned that ASCII matrix data is also ok. The "trick" here is to plot data with lines where the data is "interrupted" by empty lines, basically drawing single points. Check this in case you need to get your datafile 1:1 into a datablock.
However, if it is not already strange enough, it seems to work for png and gif terminal but not for pngcairo or wxt.
I guess the workaround is probably slow and inefficient but at least it creates the desired output. I'm not sure if there is a limit on size. Tested with 100x100 pixels with Win7, gnuplot 5.2.6. Comments and improvements are welcome.
Code:
### pixel image from matrix data without strange white border
reset session
SizeX = 100
SizeY = 100
set terminal png size SizeX,SizeY
set output "tbPixelImage.png"
# generate some random matrix data
set print $Data2
do for [y=1:SizeY] {
Line = ''
do for [x=1:SizeX] {
Line = Line.sprintf(" %9d",int(rand(0)*0x01000000)) # random color
}
print Line
}
set print
# print $Data2
# convert matrix data into x y z data with empty lines inbetween
set print $Data3
do for [y=1:SizeY] {
do for [x=1:SizeX] {
print sprintf("%g %g %s", x, y, word($Data2[y],x))
print ""
}
}
set print
# print $Data3
set margins 0,0,0,0
unset colorbox
unset border
unset key
unset tics
set xrange[1:SizeX]
set yrange[1:SizeY]
plot $Data3 u 1:2:3 w l lw 1 lc rgb var notitle
set output
### end of code
Result: (100x100 pixels)
(enlarged with black background):
Image with 400x200 pixels (takes about 22 sec on my 8 year old laptop).
What I ended up actually using to get what I needed even though the question / bounty asks for a gnuplot solution:
matplotlib has a function matplotlib.pyplot.imsave which does what I was looking for... i.e. plotting 'just data pixels' and no extras like borders, margins, axes, etc. Originally I only knew about matplotlib.pyplot.imshow and had to pull a lot of tricks to eliminate all the extras from the image file and prevent any interpolation/smoothing etc (and therefore turned to gnuplot at a certain point). With imsave it's fairly easy, so I'm back to using matplotlib for an easy yet still flexible (in terms of colormap, scaling, etc) solution for 'pixel exact' plots. Here's an example:
#!/usr/bin/env python3
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
nx = 400
ny = 200
data = np.fromfile('T.dat', dtype=np.float32, count=nx*ny)
data = data.reshape((nx,ny), order='F')
matplotlib.image.imsave('T.png', np.transpose(data), origin='lower', format='png')
OK, here is another possible solution (I separated it from my first cumbersome approach). It creates the plot immediately, less than a second. No renaming necessary or creation of a useless file.
I guess key is to use term png and ps 0.1.
I don't have a proof but I think ps 1 would be ca. 6 pixels large and would create some overlap and/or white pixels at the corner. Again, for whatever reason it seems to work with term png but not with term pngcairo.
What I tested (Win7, gnuplot 5.2.6) is a binary file having the pattern 00 00 FF repeated all over (I can't display null bytes here). Since gnuplot apparently reads 4 bytes per array item (format="%d"), this leads to an alternating RGB pattern if I am plotting with lc rgb var.
In the same way (hopefully) we can figure out how to read format="%f" and use it together with a color palette. I guess that's what you are looking for, right?
Further test results, comments, improvements and explanations are welcome.
Code:
### pixel image from matrix data without strange white border
reset session
SizeX = 400
SizeY = 200
set terminal png size SizeX,SizeY
set output "tbPixelImage.png"
set margins 0,0,0,0
unset colorbox
unset border
unset key
unset tics
set xrange[0:SizeX-1]
set yrange[0:SizeY-1]
plot "tbBinary.dat" binary array=(SizeX,SizeY) format="%d" w p pt 5 ps 0.1 lc rgb var
### end of code
Result:
I have these two functions in my program:
def depict_ph_increase(x,y,color, imobject):
program_print(color)
draw = PIL.ImageDraw.Draw(imobject)
draw.text((x, y),color,(255,255,255))
imobject.save('tmp-out.gif')
im_temp = PIL.Image.open("tmp-out.gif")#.convert2byte()
im_temp = im_temp.resize((930, 340), PIL.Image.ANTIALIAS)
MAP_temp = ImageTk.PhotoImage(im_temp)
map_display_temp = Label(main, image=MAP_temp)
map_display_temp.image = MAP_temp # keep a reference!
map_display_temp.grid(row=4,column=2, columnspan=3)
def read_temp_pixels(temperature_file, rngup, rngdown):
temp_image_object = PIL.Image.open(temperature_file)
(length, width) = get_image_size(temp_image_object)
(rngxleft, rngxright) = rngup
(rngyup,rngydown) = rngdown
print 'the length and width is'
print length, width
hotspots = 5;
for hotspot in range(0,hotspots):
color = "#ffffff"
while color == "#ffffff" or color == "#000000" or color == "#505050" or color == "#969696":
yc = random.randint(rngxleft, rngxright)
xc = random.randint(rngyup,rngydown)
color = convert_RGB_HEX(get_pixel_color(temp_image_object, xc, yc))
depict_ph_increase(xc,yc,color, temp_image_object)
The bottom one calls the top one. Their job is to read in this image:
It then randomly selects a few pixels, grabs their colors, and writes the hex values of the colors on top. But, when it redisplays the image, it gives me this garbage:
Those white numbers up near the upper right corner are the hex values its drawing. Its somehow reading the values from the corrupted image, despite the fact that I don't collect the values until AFTER I actually call the ImageDraw() method. Can someone explain to me why it is corrupting the image?
Some background--the get_pixel_color() function is used several other times in the program and is highly accurate, its just reading the pixel data from the newly corrupted image somehow. Furthermore, I do similar image reading (but not writing) at other points in my code.
If there is anything I can clarify, or any other part of my code you want to see, please let me know. You can also view the program in its entirety at my github here: https://github.com/jrfarah/coral/blob/master/src/realtime.py It should be commit #29.
Other SO questions I have examined, to no avail: Corrupted image is being saved with PIL
Any help would be greatly appreciated!
I fixed the problem by editing this line:
temp_image_object = PIL.Image.open(temperature_file)
to be
temp_image_object = PIL.Image.open(temperature_file).convert('RGB')
I'm using Geometric mean filter to remove noise instead of median filter as image quality goes off in former case. code shown below is a part of m-file to remove noise.
fname = getappdata(0, 'fname');
[a, map] = imread(fname);
x = ind2rgb(a, map);
b = im2double(x);
w=fspecial('gaussian',[3,3]);
geom=exp(imfilter(log(b),ones(3,3),'replicate')).^(1/3/3);
fname=imfilter(b,w,'replicate');
axes(handles.axes1);
imshow(fname);
If i press push button which is named 'Remove Noise' above code get executed irrespective of image quality/property. In the sense even if no noise is present, image will be subjected to filter.
My question, is there any way to detect whether noise is present or not, so that the moment i pressed push button if no Noise in image it should display a message stating 'NO NOISE TO REMOVE' automatically.
There is no direct way to determine whether an image is noisy or not.
However, you can compare resulting image fname with the input image b in such a way that if their difference is lower than a certain threshold, then it can be decided that denoising operation has not changed image effectively and there is not much noise in the original image like:
threshold_ratio = 0.2; % to be decided experimentally
difference_ratio = sum(sum((fname - b).^2)) / sum(sum(b.^2));
if difference_ratio < threshold_ratio
disp('NO NOISE TO REMOVE');
end
I made a contourfm plot with white contour lines.
I used 'LineColor', 'white' but in a movie, the white lines propagate after each image instead of redrawing. The colors on the image itself redraws automatically. What am I doing wrong?
Also, when viewing the image, it shows up small on the top left hand corner. A similar script before did not cause this issue. Anyone know why?
% Create movie
nFrames = 893; % Number of frames
for k = 1:nFrames % Create movie
% Eqdconic script
% Define figure and axes
fg1 = figure(1);
axesm('MapProjection','eqdconic', 'MapParallels', [], 'MapLatLimit',[-79.625 -59.625],'MapLonLimit',[190.625 250.625])
framem on; gridm on; mlabel on; plabel on; hold all;
% Plot data
frame = dataSST_movie(:,:,k);
image = contourfm(Y,X,frame, 'LineColor', 'white'); % Change contour lines to white
mov(k) = getframe(gcf);
end
close(gcf)
% % Save as AVI file
movie2avi(mov, 'SST_20110101to20130611_0.25grid.avi', 'compression', 'none', 'fps', 4);
The image = contourfm() part is what I'm talking about; is there some command like redraw that I need to use?
Just use clf before end. As for the size issue, check MapLatLimit and MapLonLimit. If they are correct, it should work.
Let's say my image is img=zeros(100,100,3), my outputs are several ellipse which i get using a created function [ret]=draw_ellipse(x,y,a,b,angle,color,img), I can display one ellipse using imshow(ret).For the moment, I'm trying to show serval ellipse in the image. But i don't know how to code it. will ‘for loop’ work or I need to hold them?
If this is related to what you were doing in your previous question, then what you need to do is to pass the result of one iteration as input to the next.
So assuming that the function [ret]=draw_ellipse(x,y,a,b,angle,color,img) you mentioned takes as input an image img and returns the same image with an ellipse drawn on it, you could do this:
%# ellipses parameters
%#x = {..}; y = {..};
%#a = {..}; b = {..};
%#angle = {..}; color = {..};
img = zeros(200,100,'uint8'); %# image to start with
for i=1:10
img = draw_ellipse(x{i},y{i}, a{i},b{i}, angle{i}, color{i}, img);
end
imshow(img)
I'm a bit unsure of what you want. You want to show several ellipse in one image, like plotting several graphs with hold on?
There is no equivalent command for images, but a simple solution is to add the ellipses into one image and show that one:
several_ellipse = ellipse1 + ellipse2 + ellipse3;
imshow(several_ellipse)
Presumably you want to pass ret as the final input to the next call to draw_ellipse.