I want to take a custom function for QGIS made in python and use it in a python script. The function came from this answer https://gis.stackexchange.com/questions/245146/getting-quantity-of-intersecting-lines-of-polygons-in-qgis and I updated it to work in QGIS3 (that wasn't hard). After I got it working as a custom function I decided it would be better if I could incorporate it in a script. I put this into the python console in QGIS using
def count_intersections(grid_layer_name, line_layer_name, feature, parent):
grid_layer = QgsProject.instance().mapLayersByName( grid_layer_name )[0]
line_layer = QgsProject.instance().mapLayersByName( line_layer_name )[0]
count = 0
for line_feat in line_layer.getFeatures():
if feature.geometry().intersects(line_feat.geometry()):
count = count + 1
return count
print(count_intersections('Grid', 'line')
And I get the error
TypeError: count_intersections() missing 2 required positional arguments: 'feature' and
'parent'
I'm not sure what to do with feature and parent parameters or how to fill them. I tried removing them completely but that didn't work either.
If I understand correctly, you want the number of line crossing every cell of a grid.
Your error means that you need 4 arguments to use your function, the grid layer name, the line layer, the feature of the grid where you are counting the intersecting lines and the parent argument.
The last argument is not relevant for PyQGIS but the grid feature is mandatory. I can propose to modify your code so you only have to give 2 arguments, the layers' name. And get the grid feature inside your function like in this snippet :
def count_intersections(grid_layer_name, line_layer_name):
grid_layer = QgsProject.instance().mapLayersByName( grid_layer_name )[0]
line_layer = QgsProject.instance().mapLayersByName( line_layer_name )[0]
for feature in grid_layer.getFeatures(): # added loop
count = 0
for line_feat in line_layer.getFeatures():
if feature.geometry().intersects(line_feat.geometry()):
count = count + 1
print(count)
count_intersections('Grid', 'Line')
I added a loop to look through each grid feature and compare it with line features. This is going to print for each cell the number of lines which cross the cell.
PS: For PyQGIS question, I recommend you to use GISStackExcange.
Related
I would like to add the sums of 5 one-column arrays in Matlab. The catch is that depending on previous inputs, any of these arrays may or may not exist, thus throwing an error when I try to add the sums of these arrays for post-processing.
After doing some digging I found the following function which I can use to return a logical statement if a certain variable exists in the workspace:
exist('my_variable','var') == 1
I'm not sure this helps me in this case though - Currently the line in which I add the sums of the various arrays looks as follows:
tot_deviation = sum(var1) + sum(var2) + sum(var3) + sum(var4) + sum(var4);
Is there a short way to add only the sums of the existing arrays without excessive loops?
Any help would be appreciated!
You can use if statements:
if ~exist('var1','var'), var1 = 0;end
if ~exist('var2','var'), var2 = 0;end
if ~exist('var3','var'), var3 = 0;end
if ~exist('var4','var'), var4 = 0;end
tot_deviation = sum(var1) + sum(var2) + sum(var3) + sum(var4) + sum(var4);
To my knowledge there is no quick way to do this in matlab. It seems to me that, depending on the structure of your code, you have the following alternatives:
1- Initialize all your variables to column arrays of zeros with something like
var = zeros(nbLines, 1);
2- Put all your columns vectors side to side in a single array and the use tot_deviation = sum(sum(MyArray)); which will work no matter how many columns and lines there is in the array.
3- If you pass your variables to a function you can check the number of inputs arguments inside the function using 'nargin' and then only proceed to sum the right number of variables.
I would recommend using the second method for it seem to me that it is the one that allows you to take the most advantage of matlab's array system which good.
The most robust solution is to initialise all of your variables to 0 at the top of the function. Then there is no chance they don't exist, and they influence the summation correctly.
Alternatively...
You could (read: shouldn't) use a really nasty eval trick here for flexibility...
vars = {'var1','var2','var3','var4'};
tot = 0;
for ii = 1:numel(vars)
if exist(vars{ii}, 'var')
tot = tot + eval(var);
end
end
I say it's "nasty" because eval should be avoided (read the linked blog). The check on the variable name existence mitigates some of the strife, but it's still not ideal.
As suggested in the MathWorks blog on evading eval, a better option would be a struct with dynamic field names. You could use almost the same syntax as above, but replace the if statement with
if isfield( myStruct, vars{ii} )
tot = tot + myStruct.(vars{ii});
end
This will avoid dynamically named variables and keep your workspace clean!
I have a structure such as:
specimen.trial1 = 1
I now want to add another trial to the specimen, so that
specimen.trial1 = 1
specimen.trial2 = 2
I can do this without a problem within the workspace and command window. But, if I'm using a function to calculate the numbers for each trial (with dynamic fields), the new field and value erases the previous one. Eg:
function [specimen] = dummy(trial,value)
specimen.(trial) = value
end
run the function:
[specimen] = dummy('trial1',1)
then run the function again with different inputs, but keeping the structure intact in the workspace
[specimen] = dummy('trial2',2)
Instead of getting a structure with 2 fields, I get just one with Trial2 being the only field. Does that make any sense? What would like is to use the outputs of a function to progressively add to a structure.
Thank you,
Chris
Yes it makes sense, because you're creating a new struct specimen within your function.
Solution: pass the the previous specimen to the function as well.
function [specimen] = dummy(specimen,trial,value)
specimen.(trial) = value
end
and call:
[specimen] = dummy(specimen,'trial1',1)
or alternativly leave out the assignment at all and use the following
function [output] = dummy(value)
output = value
end
and call:
[specimen.trail1] = dummy(1)
which really depends on what you actually want to do. Put passing a name to a function which uses this name to define a struct is a little pointless unless you "use" that name otherwise. Also if you want to have input-dependent dynamic names you'd also go with the first alternative
I have written a macro for ImageJ/FIJI to deconvolve my confocal microscopy images and run the "3D Object Counter" plugin. The macro successfully runs all required commands and saves all required data in the specified places.
However, I have found that the 3D-OC autothreshold (as shown in the plugin dialog box) is to stringent resulting in objects being lost or divided.
To remedy this I would like to reduce the autothreshold by a predetermined function something similar to what was done here (from:How to get threshold value used by auto threshold Plugin) which resulted in this code:
setAutoThreshold();
getThreshold(lower,upper);
v=setThreshold(lower,upper*0.5);
run("3D Objects Counter", "threshold="v" slice=10 min.=400 max.=20971520 objects statistics summary");
The idea was to call the AutoThreshold values, modify them and set them to a variable. However when these lines are run the following error is returned:
Number or numeric function expected in line 3.
v=<setThreshold>(lower,upper*0.5);
And if the variable is inserted directly into the threshold key for run(3D-OC) the following msg is encountered:
Numeric value expected in run() function
Key:"threshold"
Value or variable name:"setThreshold(lower,upper*0.5"
Any suggestions or help on how to designate the 3D-OC threshold value as a variable as described would be greatly appreciated (as would any work arounds of course :) ).
Cheers
Edit: After testing Jan's response below (which works perfectly), it appears I need to call the threshold set by the 3D-OC plugin. Anyone know how to do this?
The getThreshold(lower, upper) function returns the lower and upper threshold levels in the provided variables. There is no need to assign any value to a new variable, and as you observed, setThreshold does not have any return value.
Instead, you can use the value(s) returned from getThreshold and use them as parameters in the run method (in the correct way, by string concatenation, see here):
setAutoThreshold();
getThreshold(lower, v);
run("3D Objects Counter", "threshold=" + v + " slice=10 min.=400 max.=20971520 objects statistics summary");
Alternatively, you can use &v in the second parameter to avoid string concatenation in the last line (see the documentation for the run() macro function):
run("3D Objects Counter", "threshold=&v slice=10 min.=400 max.=20971520 objects statistics summary");
You might have to use the lower instead of the upper threshold value, depending on whether you count bright or dark objects.
I've been looking throught the documentation, but can't seem to find the bit I want.
I have a for loop and I would like to be able to view every value in the for loop.
for example here is a part of my code:
for d = 1 : nb
%for loop performs blade by blade averaging and produces a column vector
for cc = navg : length(atbmat);
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg;
atbvec2(:,cc) = atb2;
end
%assigns column vector 'atbvec2' to the correct column of the matrix 'atbmat2'
atbmat2(d,1:length(atbvec2)) = atbvec2;
end
I would like to view every value of atb2. I'm a python user(new to MATLAB) and would normally use a simple print statement to find this.
I'm sure there is a way to do it, but I can't quite find how.
Thankyou in advance.
you can use disp in Matlab to print to the screen but you might want to use sprintf first to format it nicely. However for debugging you're better off using a break point and then inspect the variable in the workspace browser graphically. To me, this is one of Matlab's best features.
Have a look at the "Examine Values" section of this article
The simplest way to view it everywhere is to change this line:
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg;
Into this, without semicolon:
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg
That being said, given the nature of your calculation, you could get the information you need as well by simply storing every value of abt2 and observing them afterwards. This may be done in atbmat2 already?
If you want to look at each value at the time it happens, consider setting a breakpoint or conditional breakpoint after the line where abt2 is assigned.
I am trying to create a function call graph for around 500 matlab src files. I am unable to find any tools which could help me do the same for multiple src files.
Is anyone familiar with any tools or plugins?
In case any such tools are not available, any suggestions on reading 6000 lines of matlab code
without documentation is welcome.
Let me suggest M2HTML, a tool to automatically generate HTML documentation of your MATLAB m-files. Among its feature list:
Finds dependencies between functions and generates a dependency graph (using the dot tool of GraphViz)
Automatic cross-referencing of functions and subfunctions with their definition in the source code
Check out this demo page to see an example of the output of this tool.
I recommend looking into using the depfun function to construct a call graph. See http://www.mathworks.com/help/techdoc/ref/depfun.html for more information.
In particular, I've found that calling depfun with the '-toponly' argument, then iterating over the results, is an excellent way to construct a call graph by hand. Unfortunately, I no longer have access to any of the code that I've written using this.
I take it you mean you want to see exactly how your code is running - what functions call what subfunctions, when, and how long those run for?
Take a look at the MATLAB Code Profiler. Execute your code as follows:
>> profile on -history; MyCode; profile viewer
>> p = profile('info');
p contains the function history, From that same help page I linked above:
The history data describes the sequence of functions entered and exited during execution. The profile command returns history data in the FunctionHistory field of the structure it returns. The history data is a 2-by-n array. The first row contains Boolean values, where 0 means entrance into a function and 1 means exit from a function. The second row identifies the function being entered or exited by its index in the FunctionTable field. This example [below] reads the history data and displays it in the MATLAB Command Window.
profile on -history
plot(magic(4));
p = profile('info');
for n = 1:size(p.FunctionHistory,2)
if p.FunctionHistory(1,n)==0
str = 'entering function: ';
else
str = 'exiting function: ';
end
disp([str p.FunctionTable(p.FunctionHistory(2,n)).FunctionName])
end
You don't necessarily need to display the entrance and exit calls like the above example; just looking at p.FunctionTable and p.FunctionHistory will suffice to show when code enters and exits functions.
There are already a lot of answers to this question.
However, because I liked the question, and I love to procrastinate, here is my take at answering this (It is close to the approach presented by Dang Khoa, but different enough to be posted, in my opinion):
The idea is to run the profile function, along with a digraph to represent the data.
profile on
Main % Code to be analized
p = profile('info');
Now p is a structure. In particular, it contains the field FunctionTable, which is a structure array, where each structure contains information about one of the calls during the execution of Main.m. To keep only the functions, we will have to check, for each element in FunctionTable, if it is a function, i.e. if p.FunctionTable(ii).Type is 'M-function'
In order to represent the information, let's use a MATLAB's digraph object:
N = numel(p.FunctionTable);
G = digraph;
G = addnode(G,N);
nlabels = {};
for ii = 1:N
Children = p.FunctionTable(ii).Children;
if ~isempty(Children)
for jj = 1:numel(Children)
G = addedge(G,ii,Children(jj).Index);
end
end
end
Count = 1;
for ii=1:N
if ~strcmp(p.FunctionTable(ii).Type,'M-function') % Keep only the functions
G = rmnode(G,Count);
else
Nchars = min(length(p.FunctionTable(ii).FunctionName),10);
nlabels{Count} = p.FunctionTable(ii).FunctionName(1:Nchars);
Count = Count + 1;
end
end
plot(G,'NodeLabel',nlabels,'layout','layered')
G is a directed graph, where node #i refers to the i-th element in the structure array p.FunctionTable where an edge connects node #i to node #j if the function represented by node #i is a parent to the one represented by node #j.
The plot is pretty ugly when applied to my big program but it might be nicer for smaller functions:
Zooming in on a subpart of the graph:
I agree with the m2html answer, I just wanted to say the following the example from the m2html/mdot documentation is good:
mdot('m2html.mat','m2html.dot');
!dot -Tps m2html.dot -o m2html.ps
!neato -Tps m2html.dot -o m2html.ps
But I had better luck with exporting to pdf:
mdot('m2html.mat','m2html.dot');
!dot -Tpdf m2html.dot -o m2html.pdf
Also, before you try the above commands you must issue something like the following:
m2html('mfiles','..\some\dir\with\code\','htmldir','doc_dir','graph','on')
I found the m2html very helpful (in combination with the Graphviz software). However, in my case I wanted to create documentation of a program included in a folder but ignoring some subfolders and .m files. I found that, by adding to the m2html call the "ignoreddir" flag, one can make the program ignore some subfolders. However, I didn't find an analogue flag for ignoring .m files (neither does the "ignoreddir" flag do the job). As a workaround, adding the following line after line 1306 in the m2html.m file allows for using the "ignoreddir" flag for ignoring .m files as well:
d = {d{~ismember(d,{ignoredDir{:}})}};
So, for instance, for generating html documentation of a program included in folder "program_folder" but ignoring "subfolder_1" subfolder and "test.m" file, one should execute something like this:
m2html( 'mfiles', 'program_folder', ... % set program folder
'save', 'on', ... % provide the m2html.mat
'htmldir', './doc', ... % set doc folder
'graph', 'on', ... % produce the graph.dot file to be used for the visualization, for example, as a flux/block diagram
'recursive', 'on', ... % consider also all the subfolders inside the program folders
'global', 'on', ... % link also calls between functions in different folders, i.e., do not link only the calls for the functions which are in the same folder
'ignoreddir', { 'subfolder_1' 'test.m' } ); % ignore the following folders/files
Please note that all subfolders with name "subfolder_1" and all files with name "test.m" inside the "program_folder" will be ignored.