Related
When I plot single images they appear to be skewed, but doesn't appear that way when I look at the images in 3DSlicer or another viewer. I'm not sure if there's something I should be adjusting that I'm not aware of. The below is how I converted from DICOM:
dicom2nifti.convert_directory(path_to_dicom_before, path_to_dicom_before_converted, compression=True, reorient=True)
dicom2nifti.convert_directory(path_to_dicom_post, path_to_dicom_post_converted, compression=True, reorient=True)
print(glob(path_to_dicom_before_converted + '*.nii.gz'))
nii_before = nib.load(glob(path_to_dicom_before_converted + '*.nii.gz')[0])
nii_after = nib.load(glob(path_to_dicom_post_converted + '*.nii.gz')[0])
nii_before_data = nii_before.get_fdata()
nii_after_data = nii_after.get_fdata()
fig, ax = plt.subplots(figsize=[10, 5])
plotting.plot_img(nii_before, cmap='gray', axes=ax)
plt.show()
fig, ax = plt.subplots(figsize=[10, 5])
plotting.plot_img(nii_after, cmap='gray', axes=ax)
plt.show()
plt.imshow(nii_before_data[100], cmap='bone')
plt.axis('off')
plt.show()
Affine of the first:
[[-3.19454312e-01 7.17869774e-02 3.95075195e-02 6.01478424e+01]
[ 5.83867840e-02 2.97792435e-01 -2.28872180e-01 1.27874863e+02]
[ 4.69673797e-02 1.18071720e-01 5.53225577e-01 1.12181287e+03]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
As you can see in this answer you are plotting the row 100 with all columns and all slices! Also you need to plot the pixel array nii_before_data and not the whole Nifti image nii_before which contains other types of data.
you can try:
nii_before = nib.load(glob(path_to_dicom_before_converted + '*.nii.gz')[0])
nii_after = nib.load(glob(path_to_dicom_post_converted + '*.nii.gz')[0])
nii_before_data = nii_before.get_fdata()
nii_after_data = nii_after.get_fdata()
## Same goes for nii_after_data
if(len(nii_before_data.shape)==3):
for slice_Number in range(nii_before_data.shape[2]):
plt.imshow(nii_before_data[:,:,slice_Number ])
plt.show()
if(len(nii_before_data.shape)==4):
for frame in range(nii_before_data.shape[3]):
for slice_Number in range(nii_before_data.shape[2]):
plt.imshow(nii_before_data[:,:,slice_Number,frame])
plt.show()
If you can provide a sample Nifti Image the solution might be more precise according to your data.
I am trying to draw a pie chart from a csv file using pgf-pie. And it must be pdf-pie, because datapie does not work for me under Debian 11. It did work under Debian 10. So I'm trying pgf-pie and I'm not interested in other solutions with other packages.
\documentclass{article}
\usepackage{csvsimple}
\usepackage{pgf-pie}
\begin{document}
\begin{filecontents*}{fruit.csv}
Name,Quantity
"Apples",30
"Pears",25
"Lemons,Limes",40.5
"Peaches",34.5
"Cherries",20
\end{filecontents*}
\csvreader[]{fruit.csv}{Name = \Name, Quantity = \Quantity}{\Quantity/\Name,}
\begin{tikzpicture}
\pie[polar, explode=0.1]{
\csvreader[]{fruit.csv}{Name = \Name, Quantity = \Quantity}{\Quantity/\Name,}
}
\end{tikzpicture}
\end{document}
The first \csvreader prints
30/”Apples”,25/”Pears”,34.5/”Peaches”,20/”Cherries”,
But that is wrong, because it doesn't print 40.5/"Lemons,Limes".
And the second \csvreader hangs pdflatex for ever with this error message:
! Use of \csv#reader doesn't match its definition.
\#ifnextchar ...eserved#d =#1\def \reserved#a {#2}
\def \reserved#b {#3}\futu...
l.2091 }
Why does this not work?
For the first part the problem is that , is normally used as a separation character in the csv file, so you need to protect it inside a group:
\documentclass{article}
\usepackage{csvsimple}
\usepackage{pgf-pie}
\begin{filecontents*}[overwrite]{fruit.csv}
Name,Quantity
"Apples",30
"Pears",25
"Lemons{,}Limes",40.5
"Peaches",34.5
"Cherries",20
\end{filecontents*}
\begin{document}
\csvreader[]{fruit.csv}{Name = \Name, Quantity = \Quantity}{\Quantity/\Name,}
\end{document}
or you could use another separator to avoid the conflict:
\documentclass{article}
\usepackage{csvsimple}
\usepackage{pgf-pie}
\begin{filecontents*}[overwrite]{fruit.csv}
Name;Quantity
"Apples";30
"Pears";25
"Lemons,Limes";40.5
"Peaches";34.5
"Cherries";20
\end{filecontents*}
\begin{document}
\csvreader[separator=semicolon]{fruit.csv}{Name = \Name, Quantity = \Quantity}{\Quantity/\Name,}
\end{document}
And for the pie chart problem, you don't actually need the pgf-pie package. Instead you could use the example from the csvsimple documentation:
\documentclass{article}
\usepackage{csvsimple}
\usepackage{pgf-pie}
\begin{filecontents*}[overwrite]{fruit.csv}
Name,Quantity
"Apples",30
"Pears",25
"Lemons{,}Limes",40.5
"Peaches",34.5
"Cherries",20
\end{filecontents*}
\begin{document}
% From the csvsimple doc:
% This example needs the packages tikz, xcolor, calc
\definecolorseries{myseries}{rgb}{step}[rgb]{.95,.85,.55}{.17,.47,.37}
\resetcolorseries{myseries}%
% a pie slice
\newcommand{\slice}[4]{
\pgfmathsetmacro{\midangle}{0.5*#1+0.5*#2}
\begin{scope}
\clip (0,0) -- (#1:1) arc (#1:#2:1) -- cycle;
\colorlet{SliceColor}{myseries!!+}%
\fill[inner color=SliceColor!30,outer color=SliceColor!60] (0,0) circle (1cm);
\end{scope}
\draw[thick] (0,0) -- (#1:1) arc (#1:#2:1) -- cycle;
\node[label=\midangle:#4] at (\midangle:1) {};
\pgfmathsetmacro{\temp}{min((#2-#1-10)/110*(-0.3),0)}
\pgfmathsetmacro{\innerpos}{max(\temp,-0.5) + 0.8}
\node at (\midangle:\innerpos) {#3};
}
% sum of amounts
\csvreader[before reading=\def\mysum{0}]{fruit.csv}{Quantity=\Quantity}{%
\pgfmathsetmacro{\mysum}{\mysum+\Quantity}%
}
% drawing of the pie chart
\begin{tikzpicture}[scale=3]%
\def\mya{0}\def\myb{0}
\csvreader[head to column names]{fruit.csv}{}{%
\let\mya\myb
\pgfmathsetmacro{\myb}{\myb+\Quantity}
\slice{\mya/\mysum*360}{\myb/\mysum*360}{\Quantity}{\Name}
}
\end{tikzpicture}%
\end{document}
I am working on a school project with Octave for calculating and plotting velocity/acceleration graphs.
I have been trying to create a subplot function so that I won't have to hardcore it for every subplot as such
subplot(3, 1, 1);
plot(time, accn);
grid;
title('Acceleration vs Time')
xlabel('Time, (s)')
ylabel('Acceleration, (m/s^2)')
subplot(3, 1, 2);
plot(time, velocity);
grid;
title('Velocity vs Time');
xlabel('Time, (s)');
ylabel('Velocity, (m/s)');
Is it possible to create a function akin to this
subplot = subplotFunction(row, column, xaxis, yaxis, header, xaxisLabel,
yaxisLabel)
subplot(3, row, column);
plot(xaxis, yaxis);
grid;
title('header')
xlabel('xaxisLabel')
ylabel('yaxisLabel')
endfunction
And then call it like this?
subplot = subplotFunction(1, 1, time, accn, 'Acceleration vs Time', 'Time, (s)', 'Acceleration, (m/s^2)')
I am quite new to using functions so my apologies :(
1;
function subplotFunction(row, column, idx, xaxis, yaxis, header, xaxisLabel, yaxisLabel)
subplot (row, column, idx);
plot (xaxis, yaxis);
grid on;
title (header)
xlabel (xaxisLabel)
ylabel (yaxisLabel)
endfunction
subplotFunction (3, 1, 1, 1:10, 11:20, "foo", "bar", "baz")
subplotFunction (3, 1, 2, 1:10, 11:20, "huhu", "haha", "hoho")
x = linspace (0, 10, 100);
subplotFunction (3, 1, 3, x, sin(x), "world", "boo", "doo")
print ("out.png")
gives
Assuming to have the following 4 datasets:
a.csv
1,1
2,3
3,5
5,6
6,9
7,9
8,10
9,12
10,13
b.csv
1,1
2,5
3,10
5,15
6,20
7,25
8,30
9,35
10,40
c.csv
1,1
2,10
3,100
5,1000
6,2000
7,5000
8,10000
9,20000
10,50000
d.csv
1,1
2,20
3,300
5,5000
6,9000
7,10000
8,15000
9,30000
10,100000
In Gnuplot I've tried to run the command stats on each of them to get the maximum value for x and y (i.e., columns 1 and 2) and to set the corresponding xrange & yrange. Unfortunately, the result is not the one I've expected.
Here is the full script:
#!/usr/bin/env gnuplot
set terminal latex
set term pngcairo enhanced size 1500,800
set output 'plot.png'
set multiplot layout 2,2
set xlabel 't' font ',16'
set ylabel '#pkt' font ',16'
set grid xtics lt 0 lw 1 lc rgb "#333333"
set grid ytics lt 0 lw 1 lc rgb "#333333"
set xtics font ',14'
set ytics font ',14'
set key font ',12'
set title font ',20'
set datafile separator ','
###
set title '(a)'
stats "a.csv" using 1:2 name "a"
set xrange [0:a_max_x]
set yrange [0:a_max_y+a_max_y*0.5]
plot "a.csv" using 1:2 title 'v1' with lines linewidth 3 linecolor rgb 'blue'
###
set title '(b)'
stats "b.csv" using 1:2 name "b"
set xrange [0:b_max_x]
set yrange [0:b_max_y+b_max_y*0.5]
plot "b.csv" using 1:2 title 'v1' with lines linewidth 3 linecolor rgb 'blue'
###
set title '(c)'
stats "c.csv" using 1:2 name "c"
set xrange [0:c_max_x]
set yrange [0:c_max_y+c_max_y*0.5]
plot "c.csv" using 1:2 title 'v1' with lines linewidth 3 linecolor rgb 'blue'
###
set title '(d)'
stats "d.csv" using 1:2 name "d"
set xrange [0:d_max_x]
set yrange [0:d_max_y+d_max_y*0.5]
plot "d.csv" using 1:2 title 'v1' with lines linewidth 3 linecolor rgb 'blue'
###
unset multiplot
and the result:
As you can see, maximum values in the plots b, c and d are not correct. Indeed, the verbose output of stats returns:
[...]
Maximum: 10.0000 [8] 13.0000 [8]
[...]
Maximum: 5.0000 [3] 15.0000 [3]
[...]
Maximum: 2.0000 [1] 10.0000 [1]
[...]
Maximum: 1.0000 [0] 1.0000 [0]
[...]
Apparently, only stats for the plot a is right. Is there anything wrong in my script?
You need you reinitialize xrange and yrange after setting them each time, because otherwise stats finds some of you points outside the range you have previously set and does not take them into account. It's the last line below:
set title '(a)'
stats "a.csv" using 1:2 name "a"
set xrange [0:a_max_x]
set yrange [0:a_max_y+a_max_y*0.5]
plot "a.csv" using 1:2 title 'v1' with lines linewidth 3 linecolor rgb 'blue'
set xrange [*:*] ; set yrange [*:*] # <--- This line after each plot will fix your issue
In your case there is no need to use stats in order to set the ranges.
Your requirements are:
Use tight limits for the xrange and the yrange. You get this with set autoscale fix.
Extend the maximum of the yrange by 50%. That is achieved with set offsets 0,0,graph 0.5,0:
#!/usr/bin/env gnuplot
set term pngcairo enhanced size 1500,800
set output 'plot.png'
set multiplot layout 2,2
set xlabel 't' font ',16'
set ylabel '#pkt' font ',16'
set grid xtics ytics lt 0 lw 1 lc rgb "#333333"
set tics font ',14'
set key font ',12'
set title font ',20'
set datafile separator ','
set style data lines
set style line 1 linewidth 3 linecolor rgb 'blue'
###
set title '(a)'
set autoscale fix
set offset 0,0,graph 0.5,0
plot "a.csv" using 1:2 title 'v1' linestyle 1
###
set title '(b)'
plot "b.csv" using 1:2 title 'v1' linestyle 1
###
set title '(c)'
plot "c.csv" using 1:2 title 'v1' linestyle 1
###
set title '(d)'
plot "d.csv" using 1:2 title 'v1' linestyle 1
###
unset multiplot
One further comment: If you're going to use a LaTeX-based terminal for your actual image, don't use latex, but rather epslatex, cairolatex, context or lua tikz, which are all much better regarding the supported features and quality.
I am using Octave.
My problem is this: I want to fill the bubbles of my scatter plot, as well as place a legend. But I get errors when I try to use 'filled', and no legend comes up when I use legend(...).
Part of my code looks like this:
%ALL SAMPLES, PHI(Signal) # THETA(Sample)=0
figure(5)
plot( Angles(:,1)([18:27]), ALL([18:27]), 10, [1 0 1]); %Magenta
hold on
scatter(Angles(:,1)([68:76]), ALL([68:76]), 10, [0 0 0]); %Black
scatter(Angles(:,1)([86:95]), ALL([86:95]), 10, [1 0 0]); %Red
scatter(Angles(:,1)([119:127]), ALL([119:127]), 10, [0 1 0]); %Green
scatter(Angles(:,1)([133:141]), ALL([133:141]), 10, [0 0 1]); %Blue
hold off
xlabel('Signal PMT angle (Sample angle at 0)');
ylabel('Normalized (signal/monitor) intensity');
legend('Control', 'Control', '1+2','Virgin','Cycle #1', 'Location','NorthEast');
title('Plot of All Samples, "-int Intensity"')
I know it should beplot( Angles(:,1)([18:27]), ALL([18:27]), 10, [1 0 1], 'filled');, but I receive errors when I do that. Also, a legend never seems to show up.
Apparently there is a problem with using legend with scatter in Octave. Based on this post:
http://octave.1599824.n4.nabble.com/Legend-in-scatter-plot-td3568032.html
the trick is to use the plot function to make scatter plot. I wrote the following function for plotting a bunch of scatter plots on the same axis.
This function takes in a bunch of cell arrays of the same length. Each element of the cell array corresponds to a separate series. The function returns a cell array of the same length containing the handle associated with each plot. The arguments of the function are explained below:
x_vals: a cell array of arrays of doubles corresponding to x values.
y_vals: a cell array of arrays of doubles corresponding to y values.
sizes: a cell array of doubles representing the size of the markers.
colors: a cell array of double arrays of length 3, representing [R, G, B] color values of the markers.
styles: a cell array of strings representing the shape of the markers.
function [handles] = scatter_series_set(x_vals, y_vals, sizes, colors, styles)
N = length(x_vals);
if ( (~ ( N == length(y_vals))) || (~ ( N == length(sizes))) || ...
(~ ( N == length(colors))) || (~ ( N == length(styles))) )
error('scatter_series_set: all arguments must be cell arrays of the same length');
end
%plot the first series
handles = cell([N, 1]);
handles{1} = plot(x_vals{1}, y_vals{1});
set(handles{1}, 'linestyle', 'none');
set(handles{1}, 'marker', styles{1});
set(handles{1}, 'markersize', sizes{1});
set(handles{1}, 'color', colors{1});
%plot additional series if present
if N > 1
hold on;
for ind = 2:N
handles{ind} = plot(x_vals{ind}, y_vals{ind});
set(handles{ind}, 'linestyle', 'none');
set(handles{ind}, 'marker', styles{ind});
set(handles{ind}, 'markersize', sizes{ind});
set(handles{ind}, 'color', colors{ind});
end
hold off;
end
end
The following example demonstrates how to use this function.
x1 = 0:(2*pi/100):(2*pi);
x2 = 2*x1;
y1 = sin(x1);
y2 = cos(x1);
y3 = sin(x2);
y4 = cos(x2);
names = {'a', 'b', 'c', 'd'};
x_vals = {x1, x1, x1, x1};
y_vals = {y1, y2, y3, y4};
sizes = {10, 10, 10, 10};
colors = {[1, 0, 0], [0, 0, 1], [0, 0, 0], [0.7071, 0, 0.7071]};
styles = {'^', 's', 'x', '+'}
scatter_series_set(x_vals, y_vals, sizes, colors, styles);
legend(names, 'location', 'southeast');
The example code produces the following plot:
The following works for me:
n = 100;
x = randn(n, 1);
y = randn(n, 1);
S = rand(n, 1)*20;
hold on
scatter(x(1:50), y(1:50), S(1:50), "red", "filled")
scatter(x(51:100), y(51:100), S(51:100), "green", "filled")
hold off
print('-depsc', 'bubbleplot.eps');
However, I'm not able to add a legend, and I didn't find any bug report or indication of a missing functionality for this. So, as an alternative, I would suggest adding marker and text to your plot.