I want to pass in foldername into the run() function and the save() function but they are within quotes and I don't know how to pass the variable names.
I generated the run() and save() function using the record command in imageJ.
The aim of this program to to automate the process of running the plugin "T2 analysis mouse" on multiple folders.
Any other tweets or help will be appreciated.
I found this online source https://imagej.nih.gov/ij/macros/ArgumentPassingDemo.txt but it does not work.
I tried multiple ways inclusing /&foldername/3 T2 &filename/3 T2 /&foldername 3 T2``/&foldername3 T2 /&filename 3 T2``/&filename3 T2
Here is the code I wrote:
function makeT2(foldername)
{
filename = foldername;
print(filename);
run("T2 Analysis mouse", "select=[/Users/Vineeth/Desktop/New stuff Feb 5/&filename 3 T2]
image=[32-bit Signed] width=256 height=128 offset=0 number=902 gap=0 little-endian");
run("Save", "save=[/Users/Vineeth/Desktop/New stuff Feb 5/&foldername3 T2/T2map.tif]");
close();
}
folders = getFileList("/Users/Vineeth/Desktop/New stuff Feb 5/");
for( i = 0; i < folders.length; i++)
{
print(folders[i]);
file = getFileList("/Users/Vineeth/Desktop/New stuff Feb 5/" + folders[i]);
for( j = 0; j < file.length; j++)
{
if(file[j] == "3 T2/")
{
print("made t2 for " + folders[i] + file[j]);
makeT2(folders[i]);
}
}
}
The various print() functions are for testing the code and the code mostly works expect for the makeT2 function.
This is the error:
java.lang.NullPointerException
at T2_Analysis_mouse.getImage(T2_Analysis_mouse.java:183)
at T2_Analysis_mouse.run(T2_Analysis_mouse.java:56)
at ij.IJ.runUserPlugIn(IJ.java:183)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.Executer.runCommand(Executer.java:124)
at ij.Executer.run(Executer.java:61)
at ij.IJ.run(IJ.java:249)
at ij.macro.Functions.doRun(Functions.java:561)
at ij.macro.Functions.doFunction(Functions.java:79)
at ij.macro.Interpreter.doStatement(Interpreter.java:203)
at ij.macro.Interpreter.doBlock(Interpreter.java:518)
at ij.macro.Interpreter.runUserFunction(Interpreter.java:278)
at ij.macro.Interpreter.doStatement(Interpreter.java:206)
at ij.macro.Interpreter.doBlock(Interpreter.java:518)
at ij.macro.Interpreter.doStatement(Interpreter.java:239)
at ij.macro.Interpreter.doIf(Interpreter.java:852)
at ij.macro.Interpreter.doStatement(Interpreter.java:215)
at ij.macro.Interpreter.doBlock(Interpreter.java:518)
at ij.macro.Interpreter.doStatement(Interpreter.java:239)
at ij.macro.Interpreter.doFor(Interpreter.java:464)
at ij.macro.Interpreter.doStatement(Interpreter.java:221)
at ij.macro.Interpreter.doBlock(Interpreter.java:518)
at ij.macro.Interpreter.doStatement(Interpreter.java:239)
at ij.macro.Interpreter.doFor(Interpreter.java:464)
at ij.macro.Interpreter.doStatement(Interpreter.java:221)
at ij.macro.Interpreter.doStatements(Interpreter.java:191)
at ij.macro.Interpreter.run(Interpreter.java:102)
at ij.macro.Interpreter.run(Interpreter.java:72)
at ij.macro.MacroRunner.run(MacroRunner.java:124)
at java.lang.Thread.run(Thread.java:695)
and this is the log after running the progran:
LeeMouseOld_30Jan18.LH1/
made t2 for LeeMouseOld_30Jan18.LH1/3 T2/
LeeMouseOld_30Jan18.LH1/
Please choose a directory where the T1 or T2 folder is the last item in the path (i.e. 5_t1 or 6_t2)
Directory return for General T folder: /Users/Vineeth/Desktop/New stuff Feb 5/&filename 3 T2/
Please adjust import settings to:
Image type: 32-bit signed
Width: 128 pixels
Height: 256 pixels
Number of images: 50 images
Check Little-endian byte order
As you can see &filename remains the same but I want the data within the variable filename to be in its place.
Use string concatenation:
run("T2 Analysis mouse", "select=[/Users/Vineeth/Desktop/New stuff Feb 5/" + filename + " 3 T2]
image=[32-bit Signed] width=256 height=128 offset=0 number=902 gap=0 little-endian");
run("Save", "save=[/Users/Vineeth/Desktop/New stuff Feb 5/" + foldername + "3 T2/T2map.tif]");
See the macro function documentation (emphasis added):
run("command"[, "options"])
Executes an ImageJ menu command. The optional second argument contains values that are automatically entered into dialog boxes (must be GenericDialog or OpenDialog). Use the Command Recorder (Plugins>Macros>Record) to generate run() function calls. Use string concatentation to pass a variable as an argument. With ImageJ 1.43 and later, variables can be passed without using string concatenation by adding "&" to the variable name. For examples, see the ArgumentPassingDemo macro.
The mentioned shortcut syntax with & does not work between square brackets [] in the option string.
A number of questions on the ImageJ forum also discuss this.
Related
I'm very new to caret package and nnet in R. I've done some projects related to ANN with Matlab before, but now I need to work with R and I need some basic help.
My input dataset has 1000 observations (in rows) and 23 variables (in columns). My output has 1000 observations and 12 variables.
Here are some sample data that represent my dataset and might help to understand my problem better:
input = as.data.frame(matrix(sample(1 : 20, 100, replace = TRUE), ncol = 10))
colnames(input) = paste ( "X" , 1:10, sep = "") #10 observations and 10 variables
output = as.data.frame(matrix(sample(1 : 20, 70, replace = TRUE), ncol = 7))
colnames(output) = paste ( "Y" , 1:7, sep = "") #10 observations and 7 variables
#nnet with caret:
net1 = train(output ~., data = input, method= "nnet", maxit = 1000)
When I run the code, I get this error:
error: invalid type (list) for variable 'output'.
I think I have to add all output variables separately (which is very annoying, especially with a lot of variables), like this:
train(output$Y1 + output$Y2 + output$Y3 + output$Y4 + output$Y5 +
output$Y6 + output$Y7 ~., data = input, method= "nnet", maxit = 1000)
This time it runs but I get this error:
Error in [.data.frame(data, , all.vars(Terms), drop = FALSE) :
undefined columns selected
I try to use neuralnet package, with the code below it works perfectly but I still have to add output variables separately :(
net1 = neuralnet(output$Y1 + output$Y2 + output$Y3 + output$Y4 +
output$Y5 + output$Y6 + output$Y7 ~., data = input, hidden=c(2,10))
p.s. since these sample data are created randomly, the neuralnet cannot converge, but in my real data it works well (in comparison to Matlab ANN)
Now, if you could help me with a way to put output variables automatically (not manually), it solves my problem (although with neuralnet not caret).
use the str() function and ascertain that its a data frame looks like you are inputting a list to the train function. This may be because of a transformation you are doing before to output.
str(output)
Without a full script of earlier steps its difficult to understand what is going on.
After trying different things and searches, I finally found a solution:
First, we must use as.formula to show the relation between our input and output. With the code below we don't need to add all the variables separately:
names1 <- colnames(output) #the name of our variables in the output
names2 = colnames(input) #the name of our variables in the input
a <- as.formula(paste(paste(names1,collapse='+', sep = ""),' ~ '
,paste(names2,collapse='+', sep = "")))
then we have to combine our input and output in a single data frame:
all_data = cbind(output, input)
then, use neuralnet like this:
net1 = neuralnet(formula = a, data = all_data, hidden=c(2,10))
plot(net1)
This is also work with the caret package:
net1 = train(a, data = all_data, method= "nnet", maxit = 1000)
but it seems neuralnet works faster (at least in my case).
I hope this helps someone else.
We have a script that defines values to names similar to #define in c. For example:
script.m:
ERR_NOERROR = 0;
ERR_FATAL = 1;
This script already exists and is used for value replacement when reading data from files.
Now we have a function (or more) that does some analysis and we would like to use the same definition in this function to avoid magic numbers. But when the script is called from the function we get an error.
Attempt to add "ERR_NOERROR" to a static workspace.
See MATLAB Programming, Restrictions on Assigning to Variables for details.
And this does not help much in the understanding of the problem.
The question is how can we make these definitions visible/usable in the functions with having to copying it every time.
Example:
function foo = bar(a)
run(script.m) %also tried running it without the run command
if a == ERR_NOERROR
foo = 5;
else
foo = 6;
end
end
edit:
There was a nested function,below in the function which I was not aware of. This explains the problem.
This kind of scoping error happens when you use nested or anonymous function within a function. The solution is well documented.
To your case, you can avoid nested function, or "Convert the script to a function and pass the variable using arguments", as the documentation suggests.
EDIT: I should have made it clear that the error occurs even if the script is not called within the nested function. Similar scenario is that, in debug mode (by setting up a break point), it will be an error if one tries to create a temporal variable to test something.
This is not a direct answer, rather a recommendation to switch to another method, which will not be mixing scope and workspace.
Instead of defining your constant in a script, you could make a class containing only constant properties. ex: code for error_codes.m:
classdef error_codes
% ---------------------------------------------------------------------
% Constant error code definition
% ---------------------------------------------------------------------
properties (Constant = true)
noerror = 0 ;
fatal = 1 ;
errorlvl2 = 2 ;
errorlvl3 = 3 ;
warning = -1 ;
% etc ...
end
end
I use this style for many different type of constants. For tidiness, I groups them all in a Matlab package directory (The directories which starts with a + character.
The added benefit of using constant class properties is the safety that the values cannot be changed in the middle of the code (your variables defined in a script could easily be overwritten by a careless user).
So assuming my file error_codes.m is placed in a folder:
\...somepath...\+Constants\error_codes.m
and of course the folder +Constants is on the MATLAB path, then to use it as in your example, instead of calling the script, just initialise an instance of the class, then use the constant values when you need them:
function foo = bar(a)
ERR = Constants.error_codes ;
if a == ERR.noerror
foo = 5;
else
foo = 6;
end
or it can works in switch statement too:
switch a
case ERR.noerror
foo = 5 ;
case ERR.warning
foo = 42 ;
case ERR.fatal
foo = [] ;
end
I wrote a macro in LibreOffice Calc and it is able to run correctly. But if I close the file and reopen, it always show #NULL! instead of the correct value. What am I missing here?
My macro code
Rem Attribute VBA_ModuleType=VBAModule
Option VBASupport 1
Function Calculate(CalType As String) As Double
'
' Calculate Macro
'
Dim i As Integer
Calc = 0
i = 1
Do While Not IsEmpty(Cells(i, 2))
If (Cells(i, 3).Value = CalType And (Cells(i,2) = "A" Or Cells(i,2) = "B")) Then
Calculate = Calculate + Cells(i, 4).Value
ElseIf (Cells(i, 3).Value = CalType And Cells(i,2) = "C") Then
Calculate = Calculate - Cells(i, 4).Value
End If
i = i + 1
Loop
'
End Function
The calling function will be something like =Calculate(J6)
The file is saved as .ods format.
The Cells call did not work at all for me. It is from VBA, not LO Basic. However I do not think that is the main problem.
LibreOffice expects that user-defined functions will be simple, only accessing the cell that contains the formula. Since the spreadsheet has not been fully loaded yet when the function is called, it is not possible to read other cells.
The workaround is to ignore errors and wait until the document is fully loaded before running the function. Take the following code as an example:
Function ReadOtherCell(row, col)
On Error GoTo ErrorHandler
oSheet = ThisComponent.CurrentController.ActiveSheet()
oCell = oSheet.getCellByPosition(row, col)
ReadOtherCell = "value is '" & oCell.getString() & "'"
Exit Function
ErrorHandler:
Reset
End Function
Sub RecalculateAll
' This is for user-defined functions that need to read the spreadsheet.
' Assign it to the "View created" event,
' because before that, the spreadsheet is not fully loaded.
ThisComponent.calculateAll
End Sub
Enter foo in A1, and =ReadOtherCell(0,0) in A2. So far, this has the same problem -- It will fail when the document is first opened.
Now, go to Tools -> Customize. In the Events tab, highlight View created. Press Macro... and find the RecalculateAll function. Then press OK.
Now when the document is closed and reopened, cell A2 should show the result value is 'foo'.
This is derived from B. Marcelly's answer at http://ooo-forums.apache.org/en/forum/viewtopic.php?f=20&t=73090&sid=f92a89d676058ab597b4b4494833b2a0.
I had the same problem.
I noticed that in the module, i had an empty Sub Main
After i 've erased it, the functions started working again
the function dir returns an array like
.
..
Folder1
Folder2
and every time I have to get rid of the first 2 items, with methods like :
for i=1:numel(folders)
foldername = folders(i).name;
if foldername(1) == '.' % do nothing
continue;
end
do_something(foldername)
end
and with nested loops it can result in a lot of repeated code.
So can I avoid these "folders" by an easier way?
Thanks for any help!
Edit:
Lately I have been dealing with this issue more simply, like this :
for i=3:numel(folders)
do_something(folders(i).name)
end
simply disregarding the first two items.
BUT, pay attention to #Jubobs' answer. Be careful for folder names that start with a nasty character that have a smaller ASCII value than .. Then the second method will fail. Also, if it starts with a ., then the first method will fail :)
So either make sure you have nice folder names and use one of my simple solutions, or use #Jubobs' solution to make sure.
A loop-less solution:
d=dir;
d=d(~ismember({d.name},{'.','..'}));
TL; DR
Scroll to the bottom of my answer for a function that lists directory contents except . and ...
Detailed answer
The . and .. entries correspond to the current folder and the parent folder, respectively. In *nix shells, you can use commands like ls -lA to list everything but . and ... Sadly, MATLAB's dir doesn't offer this functionality.
However, all is not lost. The elements of the output struct array returned by the dir function are actually ordered in lexicographical order based on the name field. This means that, if your current MATLAB folder contains files/folders that start by any character of ASCII code point smaller than that of the full stop (46, in decimal), then . and .. willl not correspond to the first two elements of that struct array.
Here is an illustrative example: if your current MATLAB folder has the following structure (!hello and 'world being either files or folders),
.
├── !hello
└── 'world
then you get this
>> f = dir;
>> for k = 1 : length(f), disp(f(k).name), end
!hello
'world
.
..
Why are . and .. not the first two entries, here? Because both the exclamation point and the single quote have smaller code points (33 and 39, in decimal, resp.) than that of the full stop (46, in decimal).
I refer you to this ASCII table for an exhaustive list of the visible characters that have an ASCII code point smaller than that of the full stop; note that not all of them are necessarily legal filename characters, though.
A custom dir function that does not list . and ..
Right after invoking dir, you can always get rid of the two offending entries from the struct array before manipulating it. Moreover, for convenience, if you want to save yourself some mental overhead, you can always write a custom dir function that does what you want:
function listing = dir2(varargin)
if nargin == 0
name = '.';
elseif nargin == 1
name = varargin{1};
else
error('Too many input arguments.')
end
listing = dir(name);
inds = [];
n = 0;
k = 1;
while n < 2 && k <= length(listing)
if any(strcmp(listing(k).name, {'.', '..'}))
inds(end + 1) = k;
n = n + 1;
end
k = k + 1;
end
listing(inds) = [];
Test
Assuming the same directory structure as before, you get the following:
>> f = dir2;
>> for k = 1 : length(f), disp(f(k).name), end
!hello
'world
a similar solution from the one suggested by Tal is:
listing = dir(directoryname);
listing(1:2)=[]; % here you erase these . and .. items from listing
It has the advantage to use a very common trick in Matlab, but assumes that you know that the first two items of listing are . and .. (which you do in this case). Whereas the solution provided by Tal (which I did not try though) seems to find the . and .. items even if they are not placed at the first two positions within listing.
Hope that helps ;)
If you're just using dir to get a list of files and and directories, you can use Matlab's ls function instead. On UNIX systems, this just returns the output of the shell's ls command, which may be faster than calling dir. The . and .. directories won't be displayed (unless your shell is set up to do so). Also, note that the behavior of this function is different between UNIX and Windows systems.
If you still want to use dir, and you test each file name explicitly, as in your example, it's a good idea to use strcmp (or one of its relations) instead of == to compare strings. The following would skip all hidden files and folder on UNIX systems:
listing = dir;
for i = 1:length(listing)
if ~strcmp(listing(i).name(1),'.')
% Do something
...
end
end
You may also wanna exclude any other files besides removing dots
d = dir('/path/to/parent/folder')
d(1:2)=[]; % removing dots
d = d([d.isdir]) % [d.isdir] returns a logical array of 1s representing folders and 0s for other entries
I used: a = dir(folderPath);
Then used two short code that return struct:
my_isdir = a([a.isdir]) Get a struct which only has folder info
my_notdir = a(~[a.isdir]) Get a struct which only has non-folder info
Combining #jubobs and #Tal solutions:
function d = dir2(folderPath)
% DIR2 lists the files in folderPath ignoring the '.' and '..' paths.
if nargin<1; folderPath = '.'; elseif nargin == 1
d = dir(folderPath);
d = d(~ismember({d.name},{'.','..'}));
end
None of the above puts together the elements as I see the question having being asked - obtain a list only of directories, while excluding the parents.
Just combining the elements, I would go with:
function d = dirsonly(folderPath)
% dirsonly lists the unhidden directories in folderPath ignoring '.' and '..'
% creating a simple cell array without the rest of the dir struct information
if nargin<1; folderPath = '.'; elseif nargin == 1
d = dir(folderPath);
d = {d([d.isdir] & [~ismember({d.name},{'.','..'})]).name}.';
end
if hidden folders in general aren't wanted the ismember line could be replaced with:
d = {d([d.isdir] & [~strncmp({d.name},'.',1)]).name}.';
if there were very very large numbers of interfering non-directory files it might be more efficient to separate the steps:
d = d([d.isdir]);
d = {d([~strncmp({d.name},'.',1)]).name}.';
We can use the function startsWith
folders = dir("folderPath");
folders = string({folders.name});
folders = folders(~startsWith(folders,"."))
Potential Solution - just remove the fields
Files = dir;
FilesNew = Files(3:end);
You can just remove them as they are the first two "files" in the structure
Or if you are actually looking for specific file types:
Files = dir('*.mat');
How can I pass the values of a specific variable to a list-processing loop inside a macro?
Let's say, as an simplified example, I've got a variable foo which contains the values 1,4,12,33 and 51.
DATA LIST FREE / foo (F2) .
BEGIN DATA
1
4
12
33
51
END DATA.
And a macro that does some stuff with those values.
For testing reasons this Macro will just echo those values.
I'd like to find a way to run a routine that works like the following:
DEFINE !testmacro (list !CMDEND)
!DO !i !IN (!list)
ECHO !QUOTE(!i).
!DOEND.
!ENDDEFINE.
!testmacro list = 1 4 12 33 51. * <- = values from foo.
This is a situation where using the Python apis would be a good choice.
I made myself a little bit familiar with Python recently :-)
So this is what I worked out.
If the variable is a numeric:
BEGIN PROGRAM PYTHON.
import spss,spssdata
foolist = [element[0] for element in spssdata.Spssdata('foo').fetchall()]
foostring = " ".join(str(int(i)) for i in foolist)
spss.Submit("!testmacro list = %(foostring)s." %locals())
END PROGRAM.
If the variable is a string:
BEGIN PROGRAM PYTHON.
import spss,spssdata
foolist = [element[0].strip() for element in spssdata.Spssdata('bar').fetchall()]
foostring = " ".join(foolist)
spss.Submit("!testmacro list = %(foostring)s." %locals())
END PROGRAM.
Variants
Duplicates removed and list is orderd
BEGIN PROGRAM PYTHON.
import spss,spssdata
foolist = sorted(set([element[0] for element in spssdata.Spssdata('foo').fetchall()]))
foostring = " ".join(str(int(i)) for i in foolist)
spss.Submit("!testmacro list = %(foostring)s." %locals())
END PROGRAM.
Duplicates removed and items in order of first appearance in the dataset
Here, I use a function which I retrieved from Peter Bengtsson's Homepage (peterbe.com)
BEGIN PROGRAM PYTHON.
import spss,spssdata
def uniquify(seq, idfun=None):
# order preserving
if idfun is None:
def idfun(x): return x
seen = {}
result = []
for item in seq:
marker = idfun(item)
if marker in seen: continue
seen[marker] = 1
result.append(item)
return result
foolist = uniquify([element[0] for element in spssdata.Spssdata('foo').fetchall()])
foostring = " ".join(str(int(i)) for i in foolist)
spss.Submit("!testmacro list = %(foostring)s." %locals())
END PROGRAM.
Non-Python Solution
Not that I recommend it, but there is even a way to do this without Python.
I got the basic Idea from a SPSS programming book, which goes as follows:
Use the WRITE command to create a text file with the wanted command and variable values and include it with the insert command.
DATASET COPY foolistdata.
DATASET ACTIVATE foolistdata.
AGGREGATE OUTFILE=* MODE=ADDVARIABLES
/BREAK
/NumberOfCases=N.
* Variable which contains the command as string in the first case.
STRING macrocommand (A18).
IF ($casenum=1) macroCommand = "!testmacro list = ".
EXECUTE.
* variable which contains a period (.) in the last case,
* for the ending of the command string.
STRING commandEnd (A1).
IF ($casenum=NumberOfCases) commandEnd = ".".
* Write the 'table' with the command and variable values into a textfile.
WRITE OUTFILE="macrocommand.txt" /macrocommand bar commandEnd.
EXECUTE.
* Macrocall.
INSERT FILE ="macrocommand.txt".