Hi Kaori,
Sorry - I made a mistake. The load function is only intended for use in the
python shell, not from a script. To load an image in a script, you can do
something like this:
overlayList.append(Image('/.../subj01/subj01-T1.nii.gz'))
On 31 July 2017 at 19:50, Kaori Ito <[log in to unmask]> wrote:
> Hi Paul,
>
> Thanks for your response and for creating such a useful tool!
>
> When I change the index to 0, it is still the same result (see below).
>
> Regarding the SliceCanvas object, can you please expand on that a little
> more? Is it an object that should be defined in fsleyes' python shell? When
> I type it into the python shell directly (after loading an image), I get an
> error saying it's not defined: 'NameError: name 'SliceCanvas' is not
> defined'
>
>
>
> makeImage.py script:
>
> >> load('/.../subj01/subj01-T1.nii.gz')
> >> print (overlayList)
> >> overlay = overlayList[0]
>
> output:
>
> fsleyes --runscript /...scripts/makeImage.py
> []
> WARNING runscript.pyc 104: __doAction - Script
> (/.../scripts/makeImage.py) could not be executed: list index out of range
>
> Traceback (most recent call last):
>
> File "fsleyes/actions/runscript.pyc", line 98, in __doAction
>
> File "fsleyes/actions/runscript.pyc", line 166, in runScript
>
> File "/.../scripts/makeImage.py", line 7, in <module>
>
> File "fsleyes/overlay.pyc", line 230, in __getitem__
>
> File "fsleyes_props/properties_value.pyc", line 1112, in __getitem__
>
> IndexError: list index out of range
>
>
> Thanks,
> Kaori
>
>
>
> On Mon, Jul 31, 2017 at 2:00 AM, paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Kaori,
>>
>> In your code, you are referring to overlaylist[1] - as python indices
>> start from 0, does it work if you change this to overlayList[0] ?
>>
>> There is no direct command to save a screenshot from the python shell,
>> although it is a good idea, so I will look at adding it in.
>>
>> In the meantime, if you can get a reference to the SliceCanvas
>> object(s), you can call its getBitmap method to get an in-memory bitmap
>> that you can then save out to file. However, if you want to save an image
>> of multiple canvases (e.g. the ortho view), you would need to generate the
>> bitmap for each canvas, and manually arrange them.
>>
>> Cheers,
>>
>> Paul
>>
>> On 29 July 2017 at 03:35, Kaori Ito <[log in to unmask]> wrote:
>>
>>> My apologies! Looks like the first part of my message didn't get posted.
>>> Here it is:
>>>
>>> Hi all,
>>>
>>> I would ideally like to use fsleyes to render the same type of images
>>> for a large number of subjects. I am able to recursively call fsleyes
>>> -render , but I would prefer to run a python script in the python shell
>>> within the program, rather than call the program again and again. I am
>>> using the standalone fsleyes version on a mac.
>>>
>>> First, is there a command I can call on the python shell to render
>>> images? (equivalent of fsleyes -render)
>>>
>>> Additionally, when I load an image and attempt to access overlayList
>>> within my script, I get the error: "list index out of range" - as if it
>>> hasn't been set (see below for full output). But, when I load the image
>>> from the script and then open up the python shell from fsleyes and type in
>>> overlayList, my image is loaded and overlayList is accessible. Can someone
>>> explain why this might be happening?
>>>
>>> Thank you in advance- any pointers would be helpful!
>>>
>>
>>
>
>
> --
> Kaori Ito, MA, OTR/L, PhD Student
> Chan Division of Occupational Science & Occupational Therapy
> University of Southern California
>
