set threshold as a function of autoThreshold - macros

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.

Related

HERE Search parameter 'r' not functioning

I am calling the public transit v8 like this
https://transit.hereapi.com/v8/stations?in=51.492597,-0.156927;r=1000&return=transport&apiKey=my_key
However, no matter what i change the r value to it continues search the default distance, whether i put it higher or lower than 500, it returns the same.
Documentation states - {lat},{lng}[;r={radius}] and all example show lat,long;r=x
I am sure I am using the correct formatting
Does anyone know why this may be?
If you try r=20 and r=50 you'll see a different number of stations returned.
There is an optional parameter maxPlaces that has some default value. If you change this it should return more stations for when r is set to larger numbers. For example:
https://transit.hereapi.com/v8/stations?in=51.492597,-0.156927;r=500&return=transport&maxPlaces=50&apiKey=my_key
The delimiter between query params is an ampersand (&) not a semicolon (;).
Maybe change ;r=1000 to &r=1000

Debugging a for loop in matlab

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.

How to reciprocate?

Actually I am coding a Matlab simulation where the AnchorID and SourceID will report to eachother. For example if I take an anchor 30 and source 50 it will collect all the agc values between these anchor and source and calculate rssi_dB and display them.Below mentioned is an example of anchor 30 and source id 50
Note: list of anchors ID's and source ID's are same. for e.g. 30 50 55 58 . These ID are both same for anchor and source.
function A30(BlinkSet)
for i=1:length(BlinkSet)
xAnchorID=30;
xSourceID=50;
a=BlinkSet{i}.AnchorID;
b=BlinkSet{i}.SourceID;
if xAnchorID==a && xSourceID==b
xagc=BlinkSet{i}.agc;
rssi_dB(i)=-(33+xagc*(89-33)/(29-1));
end
end
rssi_dB(rssi_dB==0)=[];
rssi_dBm=sum(rssi_dB(:))/length(rssi_dB);
disp([sprintf('The rssi value is %0.0f',rssi_dBm)]);
When I call the function in Matlab command window I get the rssi value of the above function.
Also my task is when I reciprocate the Anchor ID and source ID say Anchor as 50 and source as 30 like the function I have mentioned below I get an error which is mentioned after the function below.
function A50(BlinkSet)
for i=1:length(BlinkSet)
xAnchorID=50;
xSourceID=30;
a=BlinkSet{i}.AnchorID;
b=BlinkSet{i}.SourceID;
if xAnchorID==a && xSourceID==b
xagc=BlinkSet{i}.agc;
rssi_dB(i)=-(33+xagc*(89-33)/(29-1));
end
end
rssi_dB(rssi_dB==0)=[];
rssi_dBm=sum(rssi_dB(:))/length(rssi_dB);
disp([sprintf('The rssi value is %0.0f',rssi_dBm)]);
When I call this function I get an error as
??? Undefined function or variable "rssi_dB".
Error in ==> A50 at 14
rssi_dB(rssi_dB==0)=[];
Error in ==> main_reduced at 26
A50(BlinkSet);
In main function I have coded like this,
%A30(BlinkSet);
A50(BlinkSet);
Any help is highly appreciated.
In both of these functions, you only create the variable rssi_dB if execution enters the if statement within the loop (i.e., if xAnchorID==a && xSourceID==b is at some point true). Clearly, this code is never executed in your A50 function. Without knowing what is in BlinkSet it's a bit difficult to diagnose the exact problem, but this is the cause at least.
As a side note: it's not a good idea to create two separate functions to do this job when their code is almost identical. You should add an input argument to your function that allows it to do the job of both. In this particular case, all that changes is the value of xAnchorID and xSourceID, so you could just pass these in:
function srcToAnchorRssi(BlinkSet, xSourceID, xAnchorID)
% The rest of the function stays the same!
If you want to provide some defaults for these arguments, you can do, e.g.:
if nargin < 3 || isempty(xAnchorID), xAnchorID = 50; end
if nargin < 2 || isempty(xSourceID), xSourceID = 30; end
It's always a good idea to include an isempty in statements of this sort, so that your function supports syntax like myFunction(myArg1, [], myArg3). Also note that the order of the operands to || is crucial; if you did if isempty(theArgument) || nargin < theArgumentNumber and the user did not pass theArgument, then it would error in the isempty because theArgument would not exist as a local variable. We can get around this by swapping the operands' order because MATLAB is smart enough to know it doesn't have to evaluate the right operand if the left operand is true (note that this is also the case in many other programming languages).

iReport - Concatenating two variables with different evaluation time

I have two variables
$V{from} has evaluation value set to Now and
$V{to} has evaluation value set to Group.
Both seems to be working fine.
Now I need to append them. Currently I have $V{fromTo} which has expression $V{from} + "-" + $V{to}. Its evaluation time value is Group. What I want is just to simply append the current values of the two first mentioned variables. The current expression gives me the result (e.g. from = 1, to = 45)
45-45
Seems like the expression is taking the value of $V{from} evaluated during group execution time also. Any idea how to do this?
(Note, requirement does not allow me to just simply drag the two fields, i badly needed to store it in one variable)
I had the same problem. I solved setting Evaluation Time to Auto in my Text Field.

COBOL add 0 to a Variable in COMPUTE

I ran into a strange statement when working on a COBOL program from $WORK.
We have a paragraph that is opening a cursor (from DB2), and the looping over it until it hits an EOT (in pseudo code):
... working storage ...
01 I PIC S9(9) COMP VALUE ZEROS.
01 WS-SUB PIC S9(4) COMP VALUE 0.
... code area ...
PARA-ONE.
PERFORM OPEN-CURSOR
PERFORM FETCH-CURSOR
PERFORM VARYING I FROM 1 BY 1 UNTIL SQLCODE = DB2EOT
do stuff here...
END-PERFORM
COMPUTE WS-SUB = I + 0
PERFORM CLOSE-CURSOR
... do another loop using WS-SUB ...
I'm wondering why that COMPUTE WS-SUB = I + 0 line is there. My understanding is that I will always at least be 1, because of the perform block above it (i.e., even if there is an EOT to start with, I will be set to one on that initial iteration).
Is that COMPUTE line even needed? Is it doing some implicit casting that I'm not aware of? Why would it be there? Why wouldn't you just MOVE I TO WS-SUB?
Call it stupid, but with some compilers (with the correct options in effect), given
01 SIGNED-NUMBER PIC S99 COMP-5 VALUE -1.
01 UNSIGNED-NUMBER PIC 99 COMP-5.
...
MOVE SIGNED-NUMBER TO UNSIGNED-NUMBER
DISPLAY UNSIGNED-NUMBER
results in: 255. But...
COMPUTE UNSIGNED-NUMBER = SIGNED-NUMBER + ZERO
results in: 1 (unsigned)
So to answer your question, this could be classified as a technique used cast signed numbers into unsigned numbers. However, in the code example you gave it makes no sense at all.
Note that the definition of "I" was (likely) coded by one programmer and of WS-SUB by another (naming is different, VALUE clause is different for same purpose).
Programmer 2 looks like "old school": PIC S9(4), signed and taking up all the digits which "fit" in a half-word. The S9(9) is probably "far over the top" as per range of possible values, but such things concern Programmer 1 not at all.
Probably Programmer 2 had concerns about using an S9(9) COMP for something requiring (perhaps many) fewer than 9999 "things". "I'll be 'efficient' without changing the existing code". It seems to me unlikely that the field was ever defined as unsigned.
A COMP/COMP-4 with nine digits does have a performance penalty when used for calculations. Try "ADD 1" to a 9(9) and a 9(8) and a 9(10) and compare the generated code. If you can have nine digits, define with 9(10), otherwise 9(8), if you need a fullword.
Programmer 2 knows something of this.
The COMPUTE with + 0 is probably deliberate. Why did Programmer 2 use the COMPUTE like that (the original question)?
Now it is going to get complicated.
There are two "types" of "binary" fields on the Mainframe: those which will contain values limited by the PICture clause (USAGE BINARY, COMP and COMP-4); those which contain values limited by the field size (USAGE COMP-5).
With BINARY/COMP/COMP-4, the size of the field is determined from the PICture, and so are the values that can be held. PIC 9(4) is a halfword, with a maxiumum value of 9999. PIC S9(4) a halfword with values -9999 through +9999.
With COMP-5 (Native Binary), the PICture just determines the size of the field, all the bits of the field are relevant for the value of the field. PIC 9(1) to 9(4) define halfwords, pic 9(5) to 9(9) define fullwords, and 9(10) to 9(18) define doublewords. PIC 9(1) can hold a maximum of 65535, S9(1) -32,768 through +32,767.
All well and good. Then there is compiler option TRUNC. This has three options. STD, the default, BIN and OPT.
BIN can be considered to have the most far-reaching affect. BIN makes BINARY/COMP/COMP-4 behave like COMP-5. Everything becomes, in effect, COMP-5. PICtures for binary fields are ignored, except in determining the size of the field (and, curiously, with ON SIZE ERROR, which "errors" when the maxima according to the PICture are exceeded). Native Binary, in IBM Enterprise Cobol, generates, in the main, though not exclusively, the "slowest" code. Truncation is to field size (halfword, fullword, doubleword).
STD, the default, is "standard" truncation. This truncates to "PICture". It is therefore a "decimal" truncation.
OPT is for "performance". With OPT, the compiler truncates in whatever way is the most "performant" for a particular "code sequence". This can mean intermediate values and final values may have "bits set" which are "outside of the range" of the PICture. However, when used as a source, a binary field will always only reflect the value specified by the PICture, even if there are "excess" bits set.
It is important when using OPT that all binary fields "conform to PICture" meaning that code must never rely on bits which are set outside the PICture definition.
Note: Even though OPT has been used, the OPTimizer (OPT(STD) or OPT(FULL)) can still provide further optimisations.
This is all well and good.
However, a "pickle" can readily ensue if you "mix" TRUNC options, or if the binary definition in a CALLing program is not the same as in the CALLed program. The "mix" can occur if modules within the same run-unit are compiled with different TRUNC options, or if a binary field on a file is written with one TRUNC option and later read with another.
Now, I suspect Programmer 2 encountered something like this: Either, with TRUNC(OPT) they noticed "excess bits" in a field and thought there was a need to deal with them, or, through the "mix" of options in a run-unit or "across file usage" they noticed "excess bits" where there would be a need to do something about it (which was to "remove the mix").
Programmer 2 developed the COMPUTE A = B + 0 to "deal" with a particular problem (perceived or actual) and then applied it generally to their work.
This is a "guess", or, better, a "rationalisation" which works with the known information.
It is a "fake" fix. There was either no problem (the normal way that TRUNC(OPT) works) or the correct resolution was "normalisation" of the TRUNC option across modules/file use.
I do not want loads of people now rushing off and putting COMPUTE A = B + 0 in their code. For a start, they don't know why they are doing it. For a continuation it is the wrong thing to do.
Of course, do not just remove the "+ 0" from any of these that you find. If there is a "mix" of TRUNCs, a program may stop "working".
There is one situation in which I have used "ADD ZERO" for a BINARY/COMP/COMP-4. This is in a "Mickey Mouse" program, a program with no purpose but to try something out. Here I've used it as a method to "trick" the optimizer, as otherwise the optimizer could see unchanging values so would generate code to use literal results as all values were known at compile time. (A perhaps "neater" and more flexible way to do this which I picked up from PhilinOxford, is to use ACCEPT for the field). This is not the case, for certain, with the code in question.
I wonder if a testing version of the sources ever had
COMPUTE WS-SUB = I + 0
ON SIZE ERROR
DISPLAY "WS-SUB overflow"
STOP RUN
END-COMPUTE
with the range test discarded when the developer was satisfied and cleaning up? MOVE doesn't allow declarative SIZE statements. That's as much of a reason as I could see. Or perhaps developer habit of using COMPUTE to move, as a subtle reminder to question the need for defensive code at every step? And perhaps not knowing, as Joe pointed out, the SIZE clause would be just as effective without the + 0? Or a maintainer struggled with off by one errors and there was a corrective change from 1 to 0 after testing?