how to find the directory of the current python script

[Aryeh Weiss]

I am running a Python script form the Fiji script editor, an d need to
be able to import another python function that lives in the same directory.

The brute force way is:

sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
from  prune_new import prune

but I do not want a script that relies on that absolute path.

So I tried variations of IJ.getDirectory("current") and such, and none
of them produce the correct result.

I can do:

sys.path.append(IJ.getDirectory(""))
from  prune_new import prune

and select the directory, but that is annoying to do every run.

I found a solution for macros in this forum post:
https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie

where Wayne provided File.directory() for macros. I have not found the
API way to do this for a python script.

Is there a way to do it?

Thanks in advance
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Nicholas George]

Hi Aryeh,

You can find the current working directory using os.getcwd() like so:

import os
print(os.getcwd())


On 6/7/20 12:25 PM, Aryeh Weiss wrote:

> I am running a Python script form the Fiji script editor, an d need to
> be able to import another python function that lives in the same
> directory.
>
> The brute force way is:
>
> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
>
> from  prune_new import prune
>
> but I do not want a script that relies on that absolute path.
>
> So I tried variations of IJ.getDirectory("current") and such, and none
> of them produce the correct result.
>
> I can do:
>
> sys.path.append(IJ.getDirectory(""))
> from  prune_new import prune
>
> and select the directory, but that is annoying to do every run.
>
> I found a solution for macros in this forum post:
> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie 
>
>
> where Wayne provided File.directory() for macros. I have not found the
> API way to do this for a python script.
>
> Is there a way to do it?
>
> Thanks in advance
> --aryeh
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Wayne Rasband-2]

> On Jun 7, 2020, at 2:25 PM, Aryeh Weiss <[hidden email]> wrote:
>
> I am running a Python script form the Fiji script editor, an d need to be able to import another python function that lives in the same directory.

The ImageJ 1.53c18 daily build adds an IJ.getDir("file”) method that returns the directory of the most recently opened or saved file. It is similar to the File.directory() macro function. Note that IJ.getDir() is just another name for IJ.getDirectory(). Here is an example:

  IJ.log("This script was loaded from "+IJ.getDir("file"));

-wayne

> The brute force way is:
>
> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
> from  prune_new import prune
>
> but I do not want a script that relies on that absolute path.
>
> So I tried variations of IJ.getDirectory("current") and such, and none of them produce the correct result.
>
> I can do:
>
> sys.path.append(IJ.getDirectory(""))
> from  prune_new import prune
>
> and select the directory, but that is annoying to do every run.
>
> I found a solution for macros in this forum post:
> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie
>
> where Wayne provided File.directory() for macros. I have not found the API way to do this for a python script.
>
> Is there a way to do it?
>
> Thanks in advance
> --aryeh

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 07/06/2020 23:10, Wayne Rasband wrote:
>> On Jun 7, 2020, at 2:25 PM, Aryeh Weiss <[hidden email]> wrote:
>>
>> I am running a Python script form the Fiji script editor, an d need to be able to import another python function that lives in the same directory.
> The ImageJ 1.53c18 daily build adds an IJ.getDir("file”) method that returns the directory of the most recently opened or saved file. It is similar to the File.directory() macro function. Note that IJ.getDir() is just another name for IJ.getDirectory(). Here is an example:
>
>    IJ.log("This script was loaded from "+IJ.getDir("file"));
>
> -wayne

Thank you for your quick reply.

I tried this, running from the Fiji script editor.

######

import os
from os import sys

from ij import IJ

print("os.cwd gives: ", os.getcwd())    # Nicholas George's response
(thank you)
print('getDir("file") gives: ', IJ.getDir("file"))     # Wayne's response

#######

The output of the run after starting Fiji:

('os.cwd gives: ', '/home/amw')
('getDir("file") gives: ', u'/home/amw/Desktop/Fiji.app/macros/AutoRun/')

and after opening some image:

Started fileTest.py at Mon Jun 08 05:38:55 IDT 2020
('os.cwd gives: ', '/home/amw')
('getDir("file") gives: ', u'/home/amw/Pictures/')

Best regards
--aryeh

>
>
>> The brute force way is:
>>
>> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
>> from  prune_new import prune
>>
>> but I do not want a script that relies on that absolute path.
>>
>> So I tried variations of IJ.getDirectory("current") and such, and none of them produce the correct result.
>>
>> I can do:
>>
>> sys.path.append(IJ.getDirectory(""))
>> from  prune_new import prune
>>
>> and select the directory, but that is annoying to do every run.
>>
>> I found a solution for macros in this forum post:
>> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie
>>
>> where Wayne provided File.directory() for macros. I have not found the API way to do this for a python script.
>>
>> Is there a way to do it?
>>
>> Thanks in advance
>> --aryeh
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 08/06/2020 05:42, Aryeh Weiss wrote:

> On 07/06/2020 23:10, Wayne Rasband wrote:
>>> On Jun 7, 2020, at 2:25 PM, Aryeh Weiss <[hidden email]> wrote:
>>>
>>> I am running a Python script form the Fiji script editor, an d need
>>> to be able to import another python function that lives in the same
>>> directory.
>> The ImageJ 1.53c18 daily build adds an IJ.getDir("file”) method that
>> returns the directory of the most recently opened or saved file. It
>> is similar to the File.directory() macro function. Note that
>> IJ.getDir() is just another name for IJ.getDirectory(). Here is an
>> example:
>>
>>    IJ.log("This script was loaded from "+IJ.getDir("file"));
>>
>> -wayne
>
> Thank you for your quick reply.
>
> I tried this, running from the Fiji script editor.
>
> ######
>
> import os
> from os import sys
>
> from ij import IJ
>
> print("os.cwd gives: ", os.getcwd())    # Nicholas George's response
> (thank you)
> print('getDir("file") gives: ', IJ.getDir("file"))     # Wayne's response
>
> #######
>
> The output of the run after starting Fiji:
>
> ('os.cwd gives: ', '/home/amw')
> ('getDir("file") gives: ', u'/home/amw/Desktop/Fiji.app/macros/AutoRun/')
>
> and after opening some image:
>
> Started fileTest.py at Mon Jun 08 05:38:55 IDT 2020
> ('os.cwd gives: ', '/home/amw')
> ('getDir("file") gives: ', u'/home/amw/Pictures/')
>
> Best regards
> --aryeh
>

Actually, it looks like this is the intended behvior. However, it still
leaves me with a problem, because the script will not import correctly
after the last opened directory changes.

Best regrads

--aryeh

>
>>
>>
>>> The brute force way is:
>>>
>>> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
>>>
>>> from  prune_new import prune
>>>
>>> but I do not want a script that relies on that absolute path.
>>>
>>> So I tried variations of IJ.getDirectory("current") and such, and
>>> none of them produce the correct result.
>>>
>>> I can do:
>>>
>>> sys.path.append(IJ.getDirectory(""))
>>> from  prune_new import prune
>>>
>>> and select the directory, but that is annoying to do every run.
>>>
>>> I found a solution for macros in this forum post:
>>> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie 
>>>
>>>
>>> where Wayne provided File.directory() for macros. I have not found
>>> the API way to do this for a python script.
>>>
>>> Is there a way to do it?
>>>
>>> Thanks in advance
>>> --aryeh
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

Good day Aryeh,

how do you expect this to work?

Should IJ store the directory of the last file opened tat has suffix
.ijm or .py?

Not sure

Herbie

:::::::::::::::::::::::::::::::::::::::::
Am 08.06.20 um 04:46 schrieb Aryeh Weiss:

> On 08/06/2020 05:42, Aryeh Weiss wrote:
>> On 07/06/2020 23:10, Wayne Rasband wrote:
>>>> On Jun 7, 2020, at 2:25 PM, Aryeh Weiss <[hidden email]> wrote:
>>>>
>>>> I am running a Python script form the Fiji script editor, an d need
>>>> to be able to import another python function that lives in the same
>>>> directory.
>>> The ImageJ 1.53c18 daily build adds an IJ.getDir("file”) method that
>>> returns the directory of the most recently opened or saved file. It
>>> is similar to the File.directory() macro function. Note that
>>> IJ.getDir() is just another name for IJ.getDirectory(). Here is an
>>> example:
>>>
>>>    IJ.log("This script was loaded from "+IJ.getDir("file"));
>>>
>>> -wayne
>>
>> Thank you for your quick reply.
>>
>> I tried this, running from the Fiji script editor.
>>
>> ######
>>
>> import os
>> from os import sys
>>
>> from ij import IJ
>>
>> print("os.cwd gives: ", os.getcwd())    # Nicholas George's response
>> (thank you)
>> print('getDir("file") gives: ', IJ.getDir("file"))     # Wayne's response
>>
>> #######
>>
>> The output of the run after starting Fiji:
>>
>> ('os.cwd gives: ', '/home/amw')
>> ('getDir("file") gives: ', u'/home/amw/Desktop/Fiji.app/macros/AutoRun/')
>>
>> and after opening some image:
>>
>> Started fileTest.py at Mon Jun 08 05:38:55 IDT 2020
>> ('os.cwd gives: ', '/home/amw')
>> ('getDir("file") gives: ', u'/home/amw/Pictures/')
>>
>> Best regards
>> --aryeh
>>
> Actually, it looks like this is the intended behvior. However, it still
> leaves me with a problem, because the script will not import correctly
> after the last opened directory changes.
>
> Best regrads
>
> --aryeh
>
>
>
>>
>>>
>>>
>>>> The brute force way is:
>>>>
>>>> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
>>>>
>>>> from  prune_new import prune
>>>>
>>>> but I do not want a script that relies on that absolute path.
>>>>
>>>> So I tried variations of IJ.getDirectory("current") and such, and
>>>> none of them produce the correct result.
>>>>
>>>> I can do:
>>>>
>>>> sys.path.append(IJ.getDirectory(""))
>>>> from  prune_new import prune
>>>>
>>>> and select the directory, but that is annoying to do every run.
>>>>
>>>> I found a solution for macros in this forum post:
>>>> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie 
>>>>
>>>>
>>>> where Wayne provided File.directory() for macros. I have not found
>>>> the API way to do this for a python script.
>>>>
>>>> Is there a way to do it?
>>>>
>>>> Thanks in advance
>>>> --aryeh
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Herbie

On 08/06/2020 09:36, Herbie wrote:
> Good day Aryeh,
>
> how do you expect this to work?
>
> Should IJ store the directory of the last file opened tat has suffix
> .ijm or .py?

Good question. I wonder if the script editor has the information somewhere.

I do not mind a mechanism specific to the script editor because I am
anyway using the parameter entry syntax that is specific to it
(#@Boolean ...)

Maybe as you suggest, or even a table for each loaded script (just like
it knows the directory from which an image was loaded).

But you are correct that it is not obvious. Could be that I should
instead decide on a place to put any helper scripts that I need relative
to a directory that ImageJ knows about.

Best regards
--aryeh

>
> Not sure
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::
> Am 08.06.20 um 04:46 schrieb Aryeh Weiss:
>> On 08/06/2020 05:42, Aryeh Weiss wrote:
>>> On 07/06/2020 23:10, Wayne Rasband wrote:
>>>>> On Jun 7, 2020, at 2:25 PM, Aryeh Weiss <[hidden email]> wrote:
>>>>>
>>>>> I am running a Python script form the Fiji script editor, an d
>>>>> need to be able to import another python function that lives in
>>>>> the same directory.
>>>> The ImageJ 1.53c18 daily build adds an IJ.getDir("file”) method
>>>> that returns the directory of the most recently opened or saved
>>>> file. It is similar to the File.directory() macro function. Note
>>>> that IJ.getDir() is just another name for IJ.getDirectory(). Here
>>>> is an example:
>>>>
>>>>    IJ.log("This script was loaded from "+IJ.getDir("file"));
>>>>
>>>> -wayne
>>>
>>> Thank you for your quick reply.
>>>
>>> I tried this, running from the Fiji script editor.
>>>
>>> ######
>>>
>>> import os
>>> from os import sys
>>>
>>> from ij import IJ
>>>
>>> print("os.cwd gives: ", os.getcwd())    # Nicholas George's response
>>> (thank you)
>>> print('getDir("file") gives: ', IJ.getDir("file"))     # Wayne's
>>> response
>>>
>>> #######
>>>
>>> The output of the run after starting Fiji:
>>>
>>> ('os.cwd gives: ', '/home/amw')
>>> ('getDir("file") gives: ',
>>> u'/home/amw/Desktop/Fiji.app/macros/AutoRun/')
>>>
>>> and after opening some image:
>>>
>>> Started fileTest.py at Mon Jun 08 05:38:55 IDT 2020
>>> ('os.cwd gives: ', '/home/amw')
>>> ('getDir("file") gives: ', u'/home/amw/Pictures/')
>>>
>>> Best regards
>>> --aryeh
>>>
>> Actually, it looks like this is the intended behvior. However, it
>> still leaves me with a problem, because the script will not import
>> correctly after the last opened directory changes.
>>
>> Best regrads
>>
>> --aryeh
>>
>>
>>
>>>
>>>>
>>>>
>>>>> The brute force way is:
>>>>>
>>>>> sys.path.append(os.path.abspath("/home/amw/Desktop/projects/alerding/summer2020"))
>>>>>
>>>>> from  prune_new import prune
>>>>>
>>>>> but I do not want a script that relies on that absolute path.
>>>>>
>>>>> So I tried variations of IJ.getDirectory("current") and such, and
>>>>> none of them produce the correct result.
>>>>>
>>>>> I can do:
>>>>>
>>>>> sys.path.append(IJ.getDirectory(""))
>>>>> from  prune_new import prune
>>>>>
>>>>> and select the directory, but that is annoying to do every run.
>>>>>
>>>>> I found a solution for macros in this forum post:
>>>>> https://forum.image.sc/t/does-anyone-have-an-elegant-way-to-id-the-folder-a-macro-is-run-from/7924?u=herbie 
>>>>>
>>>>>
>>>>> where Wayne provided File.directory() for macros. I have not found
>>>>> the API way to do this for a python script.
>>>>>
>>>>> Is there a way to do it?
>>>>>
>>>>> Thanks in advance
>>>>> --aryeh
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>>
>>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html