X for plots and slicing char arrays

code/02-arrays.m

@@ -45,21 +45,19 @@
 
   M(1:4, :)
   M(:, 6:end)
+  N = M(:)
+  size(N)
 
 % ! Challenge:
 % ## Master indexing
 % !! Solution:
   M(2:3:end, :)
 
 
-
-% ! Challenge:
 % ## Slicing character arrays
   element = 'oxygen';
   disp("first three characters: " + element(1:3))
   disp("last three characters: " + element(4:6))
-% !! Solution:
-
-
+  element(1:2:end)
 
 

code/04-plotting.m

@@ -3,15 +3,16 @@
 
 
 % ## Plotting
-  plot(1:40,per_day_mean)
+  day_of_trial = 1:40;
+  plot(day_of_trial, per_day_mean)
 
 
 
 
   title("Daily average inflammation")
   xlabel("Day of trial")
   ylabel("Inflammation")
-  plot(per_day_max)
+  plot(day_of_trial, per_day_max)
   title("Maximum inflammation per day")
   ylabel("Inflammation")
   xlabel("Day of trial")
@@ -20,57 +21,62 @@
   edit src/single_plot.m
   addpath("src")
 
-  plot(per_day_min)
+  day_of_trial = 1:40;
+  plot(day_of_trial, per_day_min)
   title("Minimum inflammation per day")
   ylabel("Inflammation")
   xlabel("Day of trial")
 % ## Multiple lines in a plot
   copyfile("src/single_plot.m","src/multiline_plot.m")
-  plot(per_day_mean,DisplayName="Mean")
+  day_of_trial = 1:40;
+  plot(day_of_trial, per_day_mean, DisplayName="Mean")
   legend
   title("Daily average inflammation")
   xlabel("Day of trial")
   ylabel("Inflammation")
   hold on
-  plot(patient_5,DisplayName="Patient 5")
+  plot(day_of_trial, patient_5, DisplayName="Patient 5")
   hold off
 
 % ! Challenge:
 % ## Patients 3 & 4
 % !! Solution:
-  plot(per_day_mean,DisplayName="Mean")
+  day_of_trial = 1:40;
+  plot(day_of_trial, per_day_mean, DisplayName="Mean")
   legend
   title("Daily average inflammation")
   xlabel("Day of trial")
   ylabel("Inflammation")
   hold on
-  plot(patient_data(3,:),DisplayName="Patient 3")
-  plot(patient_data(4,:),DisplayName="Patient 4")
+  plot(day_of_trial, patient_data(3,:), DisplayName="Patient 3")
+  plot(day_of_trial, patient_data(4,:), DisplayName="Patient 4")
   hold off
 
 
 % ## Multiple plots in a figure
   edit src/tiled_plot.m
+  day_of_trial = 1:40;
   tiledlayout(1, 2)
   nexttile
-  plot(per_day_max)
+  plot(day_of_trial, per_day_max)
   title("Max")
   xlabel("Day of trial")
   ylabel("Inflamation")
   nexttile
-  plot(per_day_min)
+  plot(day_of_trial, per_day_min)
   title("Min")
   xlabel("Day of trial")
   ylabel("Inflamation")
+  day_of_trial = 1:40;
   tlo=tiledlayout(1, 2);
   title(tlo,"Per day data")
   xlabel(tlo,"Day of trial")
   ylabel(tlo,"Inflamation")
   nexttile
-  plot(per_day_max)
+  plot(day_of_trial, per_day_max)
   title("Max")
   nexttile
-  plot(per_day_min)
+  plot(day_of_trial, per_day_min)
   title("Min")
 
 % ## Where is the `nexttile`?

code/extract_episodes_code.m

@@ -5,6 +5,11 @@ function extract_episodes_code(episode_names,q)
 %   Otherwise, it will iterate through the "*.md" files in "episodes/"
 %
 %   The extracted code blocks are saved in the "code" folder.
+%
+%   Usage:
+%   - Add the 'code' and 'episodes' directories to MATLAB's path.
+%   - To extract the code from all episodes, run on the console:
+%     >> extract_episodes_code()
 
     quiet=false;
     if ~exist("episode_names","var")

episodes/02-arrays.md

@@ -346,6 +346,29 @@ ans =
    62   63    1
 ```
 
+or even the whole matrix. Try for example:
+
+```matlab
+>> N = M(:)
+```
+and you'll see that it returns all the elements of M.
+The result, however, is a column vector, not a matrix.
+We can make sure that the result of `M(:)` has 8x8=64 elements
+by using the function [size](https://uk.mathworks.com/help/matlab/ref/size.html),
+which returns the dimensions of the array given as an input:
+```matlab
+>> size(N)
+```
+```output
+ans =
+   64    1
+```
+So it has 64 rows and 1 column.
+Effectively, then, `M(:)` 'flattens' the array into a column vector.
+The order of the elements in the resulting vector comes from appending each column of the original array in turn.
+This is the result of something called [linear indexing](https://uk.mathworks.com/company/technical-articles/matrix-indexing-in-matlab.html),
+which is a way of accessing elements of an array by a single index.
+
 :::::::::::::::::::::::::::::::::::::::  challenge
 
 ## Master indexing
@@ -371,8 +394,6 @@ ans =
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-:::::::::::::::::::::::::::::::::::::::  challenge
-
 ## Slicing character arrays
 
 A subsection of an array is called a [slice]({{ page.root }}/reference.html#slice).
@@ -389,71 +410,20 @@ first three characters: oxy
 last three characters: gen
 ```
 
-1. Use slicing to:
-  - Select all elements from the 3rd to the last one.
-  - Find out what is the value of `element(1:2:end)`?
-  - Figure out how would you get all characters except the first and last?
-
-2. We used the single colon operator `:` in the indices to get all the available column or row numbers,
-   but we can also use it like this: `M(:)`. What do you think will happen?
-   How many elements does `M(:)` have?
-   What would happen if we use it for the element variable? Compare the result from `element` and `element(:)`.
-   Are there any differences?
-
-:::::::::::::::  solution
-
-
-1) Exercises using slicing
-
-  - To select all elements from 3rd to last we can use start our range at `3` and use the keyword `end`:
-    ```matlab
-    >> element(3:end)
-    ```
-    ```output
-    ans =
-        'ygen'
-    ```
-
-  - The command `element(1:2:end)` starts at the first character, selects every other element (notice the interval is 2),
-    and goes all the way until the last element, so:
-    ```matlab
-    >> element(1:2:end)
-    ```
-    ```output
-    ans =
-        'oye'
-    ```
-
-  - To select each character starting with the second we set the start at `2`,
-    and to not include the last one we can finish at `end-1`:
-    ```matlab
-    >> element(2:end-1)
-    ```
-    ```output
-    ans =
-        'xyge'
-    ```
-
-2) The colon operator gets all the elements that it can find, and so using it as `M(:)` returns all the elements of M.
-   We can make sure that the result of `M(:)` has 8x8=64 elements
-   by using the function [size](https://uk.mathworks.com/help/matlab/ref/size.html),
-   which returns the dimensions of the array given as an input:
-   ```matlab
-   >> size(M(:))
-   ```
-   ```output
-   ans =
-       64    1
-   ```
-   So it has 64 rows and 1 column. Efectively, then, `M(:)` 'flattens' the array into a column vector.
-   The order of the elements in the resulting vector comes from appending each column of the original array in turn.
-   Therefore, the last 8 elements we see if we evaluate `M(:)` correspond to the last column of `M`, for example.
-
-   The difference between evaluating `element` and `element(:)` is that the former is a row vector, and the latter a column vector.
+And we can use all the tricks we have learned to select the data we want.
+For example, to select every other character we can use the colon operator with an increment of 2:
+```matlab
+>> element(1:2:end)
+```
+```output
+ans =
+    'oye'
+```
 
-:::::::::::::::::::::::::
+We can also use the colon operator to access all the elements of the array,
+but you'll notice that the only difference between evaluating `element` and `element(:)`
+is that the former is a row vector, and the latter a column vector.
 
-::::::::::::::::::::::::::::::::::::::::::::::::::
 
 
 

episodes/04-plotting.md

@@ -32,11 +32,14 @@ We will start by exploring the function `plot`.
 The most common usage is to provide two vectors, like `plot(X,Y)`.
 Lets start by plotting the average inflammation across patients over time.
 For the `Y` vector we can provide `per_day_mean`,
-and for the `X` vector we can simply use the day number,
-which we can generate as a range with `1:40`.
+and for the `X` vector we want to use the number of the day in the trial,
+which we can generate as a range with:
+```matlab
+>> day_of_trial = 1:40;
+```
 Then our plot can be generated with:
 ```matlab
->> plot(1:40,per_day_mean)
+>> plot(day_of_trial, per_day_mean)
 ```
 
 :::::::::::::::::::::::::::::::::::::::::  callout
@@ -53,7 +56,7 @@ In most cases, however, using the indices on the x axis is not desireable.
 :::::::::::::::::::::::::::::::::::::::::  callout
 
 **Note:** We do not even need to have the vector saved as a variable.
-We would obtain the same plot with the command `plot(mean(patient_data, 1))`.
+We would obtain the same plot with the command `plot(1:40, mean(patient_data, 1))`, or `plot(mean(patient_data, 1))`.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -75,7 +78,7 @@ As we expected, this figure tells us way more than the numbers we had seen in th
 Let's have a look at two other statistics: the maximum and minimum
 inflammation per day across all patients.
 ```matlab
->> plot(per_day_max)
+>> plot(day_of_trial, per_day_max)
 >> title("Maximum inflammation per day")
 >> ylabel("Inflammation")
 >> xlabel("Day of trial")
@@ -116,7 +119,8 @@ Try copying and pasting the plot commands for the max inflammation on the script
 Because we now have a script, it should be much easier to change the plot to the minimum inflammation:
 
 ```matlab
->> plot(per_day_min)
+>> day_of_trial = 1:40;
+>> plot(day_of_trial, per_day_min)
 >> title("Minimum inflammation per day")
 >> ylabel("Inflammation")
 >> xlabel("Day of trial")
@@ -145,7 +149,8 @@ We can specify the legend names by adding `,DisplayName="legend name here"`
 inside the plot function. We then need to activate the legend by running `legend`.
 So, to plot the mean values we first do:
 ```matlab
->> plot(per_day_mean,DisplayName="Mean")
+>> day_of_trial = 1:40;
+>> plot(day_of_trial, per_day_mean, DisplayName="Mean")
 >> legend
 >> title("Daily average inflammation")
 >> xlabel("Day of trial")
@@ -157,7 +162,7 @@ So, to plot the mean values we first do:
 Then, we can use the instruction `hold on` to add a plot for patient_5.
 ```matlab
 >> hold on
->> plot(patient_5,DisplayName="Patient 5")
+>> plot(day_of_trial, patient_5, DisplayName="Patient 5")
 >> hold off
 ```
 
@@ -178,7 +183,8 @@ Try to plot the mean across all patients and the inflammation data for patients
 The first part for the mean remains unchanged: 
 
 ```matlab
->> plot(per_day_mean,DisplayName="Mean")
+>> day_of_trial = 1:40;
+>> plot(day_of_trial, per_day_mean, DisplayName="Mean")
 >> legend
 >> title("Daily average inflammation")
 >> xlabel("Day of trial")
@@ -191,14 +197,14 @@ Now we can either save that data in a variable, or we use it directly in the plo
 
 ```matlab
 >> hold on
->> plot(patient_data(3,:),DisplayName="Patient 3")
->> plot(patient_data(4,:),DisplayName="Patient 4")
+>> plot(day_of_trial, patient_data(3,:), DisplayName="Patient 3")
+>> plot(day_of_trial, patient_data(4,:), DisplayName="Patient 4")
 >> hold off
 ```
 
 The result looks like this:
 
-![](fig/plotting_patients-3-4.svg){alt='Average inflamation and Patients 3 & 4'}
+![](fig/plotting_patients-3-4.svg){alt='Average inflammation and Patients 3 & 4'}
 
 Patient 4 seems also quite average, but patient's 3 measurements are quite noisy!
 
@@ -223,14 +229,15 @@ Lets start a new script for this topic:
 ```
 We can show the average daily min and max plots together with:
 ```matlab
+>> day_of_trial = 1:40;
 >> tiledlayout(1, 2)
 >> nexttile
->> plot(per_day_max)
+>> plot(day_of_trial, per_day_max)
 >> title("Max")
 >> xlabel("Day of trial")
 >> ylabel("Inflamation")
 >> nexttile
->> plot(per_day_min)
+>> plot(day_of_trial, per_day_min)
 >> title("Min")
 >> xlabel("Day of trial")
 >> ylabel("Inflamation")
@@ -240,15 +247,16 @@ We can show the average daily min and max plots together with:
 We can also specify titles and labels for the whole tiled layout if we assign the tiled layout to a variable 
 and pass it as a first argument to `title`, `xlabel` or `ylabel`, for example:
 ```matlab
+>> day_of_trial = 1:40;
 >> tlo=tiledlayout(1, 2);
 >> title(tlo,"Per day data")
 >> xlabel(tlo,"Day of trial")
 >> ylabel(tlo,"Inflamation")
 >> nexttile
->> plot(per_day_max)
+>> plot(day_of_trial, per_day_max)
 >> title("Max")
 >> nexttile
->> plot(per_day_min)
+>> plot(day_of_trial, per_day_min)
 >> title("Min")
 ```