File Permission Error? (Vista)

cellprofiler

#1

Hi all,

I am setting up CellProfiler on a new laptop and having some problems. I have successfully installed the developers version on a Windows Vista machine running Matlab 7.7.0 (2008b). I can run the software and have fixed the small bug with the user interface on this version. However, when i try to run an analysis, i get the following error:

[code]There was an error saving the output file. Please check whether you have permission and space to write to that location.

Stack:
AnalyzeImagesButton_Callback in C:\Program Files\CellProfiler\CellProfiler.m (4506)
gui_mainfcn in C:\Program Files\CellProfiler\CellProfiler.m (6073)
CellProfiler in C:\Program Files\CellProfiler\CellProfiler.m (55)
[/code]

What is odd is that the output file does appear for some pipelines. For example, the CreateTemplate pipe successfully outputs the image mask even though it gives this error, whilst the AnalysisPIPE gives the error and fails. Thanks in advance for your help!

I suspect it is a Vista problem. I am running as admin, and have changed the file permissions to be able to read and write the entire matlab and cellprofiler folders. Is there something simple I am failing to set correctly?
2009_01_31_CreateTemplatePIPE.mat (861 Bytes)
2009_01_31_AnalysisPIPE.mat (891 Bytes)


#2

Further work and experimentation has led me to rule out file permissions as the root of my problem. I am now wondering if there is some problem with my installation of the developers version, so i will try installing the regular version. My question is will i need to install the MCR even if i have a functioning matlab version on my computer?


#3

Hi Aidan,

Yes, if you are using the compiled version, you will need the MCR along with it. If you run into additional/similar problems as with the developers version, please let us know!
-Mark


#4

No luck running the compiled version, same errors about inability to write to the files with cellprofiler.m being the culprit. Must be a vista problem with something, i’ll dig around and see if i can find anything i’ve done wrong and keep looking into the file permissions. Are their any vista users out there that have/have not had the same problem?

Sigh. Damned forced upgrade to vista!


#5

Solved it. Apparently vista causes problems writing the .mat files as output in certain places, but not other files (e.g. the .png mask files, excel exports). Having the output folder anywhere in the C:\Program Files\CellProfiler folder is fine though, thankfully. That stumped for a while, and as is usually the case, the fix was rather obvious in hindsight!


#6

Really? That seems like a fairly non-intuitive cause, if you ask me… :smiley: Good job for finding it!

Do you know where in Vista you can set permissions for particular files in certain places? That might be good info for other Vista users in the future…
-Mark


#7

[quote=“mbray”]Really? That seems like a fairly non-intuitive cause, if you ask me… :smiley: Good job for finding it!

Do you know where in Vista you can set permissions for particular files in certain places? That might be good info for other Vista users in the future…
-Mark[/quote]

I was suspicious after it would output the .png mask file to the output folder (set in various places eg C:\Program Files, the Desktop, My Documents), and I only noticed that it was supposed to also be outputting a .mat file for that step after looking at an old folder on the removable drive from work.

I got it to work by right clicking on C:\Program Files, selecting “Properties”. Clicked the “Security” tab, and edited both the administrators account and the users account (both under my own user name) to have full control of that directory. It took a minute to change the file permissions for all files in this folder. This only worked after i made the administrator account (my account!) the owner of that directory (at the “Security” tab click “Advanced”, then find the “Owner” tab, then “Edit”, change to your account, click ok all the way out). Disclaimer: Not sure if this is the best thing to do from a security point of view, there is probably a reason it is set the way it is.

I can only assume it is part of Vista’s new file “security” functions, which are a PITA. It is all well and good if a virus or trojan can’t change your files or write to the disk, but if the user can’t either it is just frustrating!