http://imagej.273.s1.nabble.com/retrieve-variables-from-txt-file-and-run-command-tp5021572p5021623.html
thank you for the hint. I had the file close in other parts of the
macro, but totally forgot it there. Now it works with:
> Hi Chris,
>
> concerning splitting lines with "\n" as delimiter:
>
> The split function of ImageJ works independent of the type of actual
> line termination (CR, LF, or CRLF). If you replace "\n" with something
> else, it will work correctly only for files created on Linux-like
> systems, where the line terminator is LF (= "\n"). On Windows, the
> line terminator is CRLF, so you will get an extra CR ("\r", hex 0D)
> character that does not get replaced. ImageJ commands preceded by a CR
> character won't be recognized.
>
> Technical details behind it: To avoid problems with different line
> terminations, ImageJ uses BufferedReader.readLine for "split" with a
> "\n" character:
>
>
https://docs.oracle.com/javase/7/docs/api/java/io/BufferedReader.html#readLine()
>
> "A line is considered to be terminated by any one of a line feed
> ('\n'), a carriage return ('\r'), or a carriage return followed
> immediately by a linefeed."
>
> ---
>
> Concerning writing a macro and then executing it: Did you close the
> file after writing?
> You need to close a file after writing, to make sure all data are
> actually transferred to disk.
>
>
> Michael
> ________________________________________________________________
> On 10.01.19 16:15, Matti Christoph wrote:
>> Dear Michael,
>>
>> it worked, thank you! The issue was apparently the
>>
>> string2 = replace(file, delimiter, "@");
>>
>> which I included to be sure that there are no issues with the
>> replace, but after removing all goes fine.
>>
>> However, i have a follow up question. I give the user the option, to
>> save the new set values as standard settings (saves the array with
>> new data as a txt file using a for loop and print(file lines[i]);)
>> and I want to give the user the option, to re-load "default values".
>> This is achieved by opening a second txt file (default_settings.txt),
>> again add it to an array and save this one as the settings.txt file.
>> So far so good.
>>
>> file = File.open(pathset);
>> for(i=0; i<lines.length; i++) {
>> print(file, lines[i]);
>> }
>>
>> I then want to re-open the macro (call it xy.ijm), and tried this
>> with the runMacro("xy.ijm"), however there it gives me an error that
>> the file from which it reads the values is empty.
>>
>> wait(2000);
>> runMacro("xy.ijm");
>>
>> Even adding a wait(2000) after printing the new values and opening
>> the macro again didn't work. If I put an "exit()" after the print,
>> and then start the macro again by hand, the new values are propperly
>> loaded. I can leave it at that, however a totally automated way of
>> closing and re-starting the macro would be nice. Or even, say, go
>> back to line xy and start again.
>>
>> Do you have any clues how to achieve this?
>>
>> Best wishes,
>>
>> Chris
>>
>> Am 14.12.2018 um 16:40 schrieb Michael Schmid:
>>> Hi Chris,
>>>
>>> you can have a list of commands for 'run' in a file.
>>> The following works:
>>>
>>> path="/tmp/filename.txt";
>>> txt = File.openAsRawString(path);
>>> delimiter= '\n';
>>> lines = split(txt, delimiter);
>>> for (i=0; i<lines.length; i++)
>>> run(lines[i]);
>>>
>>> And the file may contain:
>>> Blobs (25K)
>>> Green
>>> Smooth
>>> Invert
>>>
>>> There should be no quotes, no spaces, no blank lines in the file.
>>> It will open the blobs sample, apply the Green LUT, smooth and
>>> invert it.
>>> Like this, it only works with 'run' commands that need no further
>>> arguments, like
>>> run("Green"): //apply green LUT
>>>
>>>
>>> If you want 'run' commands with arguments, you can use e.g. tabs to
>>> separate the name and argument:
>>>
>>> path="/tmp/filename.txt";
>>> txt = File.openAsRawString(path);
>>> delimiter= '\n';
>>> lines = split(txt, delimiter);
>>> for (i=0; i<lines.length; i++) {
>>> parts = split(lines[i],"\t");
>>> if (parts.length ==1)
>>> run(parts[0]);
>>> else if (parts.length ==2)
>>> run(parts[0], parts[1]);
>>> }
>>>
>>> Now you can process this file:
>>> Blobs (25K)
>>> Gaussian Blur... sigma=10
>>>
>>> What cannot be done so easily this way is calling macro commands
>>> other than 'run'.
>>>
>>>
>>> Michael
>>> ________________________________________________________________
>>> On 14.12.18 15:31, Matti Christoph wrote:
>>>> Dear all,
>>>>
>>>> I have a macro, helping to annotate images with scale bar, channel
>>>> names, doing a montage and so on. So far, the initial dialogue
>>>> gives the user several options, and is filled with default values.
>>>>
>>>> I like to have a text file with those variables and recall them
>>>> automatically when the Macro is started, and yes, that works.
>>>>
>>>> setOption("ExpandableArrays", true);
>>>>
>>>> mp = getDirectory("macros");
>>>> pathset = mp+"CnZsettings.txt";
>>>> string2 = newArray();
>>>> file = File.openAsRawString(pathset);
>>>> delimiter= '\n';
>>>> string2 = replace(file, delimiter, "@");
>>>> values = newArray();
>>>> values = split(string2, "@");
>>>>
>>>> However, when taking the value from the text file (e.g. Green) and
>>>> assigning to a variable:
>>>>
>>>> a=values[0];
>>>>
>>>> the run(a); or SetColor(a); to change either the channel colour or
>>>> the foreground colour don't work, giving me /Unrecognised command:
>>>> "Green"/. Retrieving however numerical values from the same .txt
>>>> file and using them e.g. for the scale bar do work.
>>>>
>>>> Do you have any suggestion where to look for a solution? I believe
>>>> that I somehow have to change the "type" of the variable or something?
>>>>
>>>> I already tried a="\""+values[0]+"\""; but this didn't work, giving
>>>> me /Unrecognised command: ""Green""/.
>>>>
>>>> I am very happy if one of you could help me.
>>>>
>>>> Best,
>>>>
>>>> Chris
>>>>
>>>>
>>>
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