[BioC] unable to readImage using EBImage package

[Dan Tenenbaum]

On Sat, Mar 3, 2012 at 2:42 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Please CC the bioconductor list. Also, please read the posting guide,
> and provide the output of the sessionInfo() function.
>
> See below.
>
> On Sat, Mar 3, 2012 at 1:04 AM, Nurdiyanah Jambari <yanadj28 at gmail.com> wrote:
>> I've correct the spelling, but I still receive the same warning message. Can
>> you help me.
>>
>>
>> On Sat, Mar 3, 2012 at 3:58 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>>
>>>
>>> On Mar 2, 2012 11:25 PM, "diyanah [guest]" <guest at bioconductor.org> wrote:
>>> >
>>> >
>>> > Hi, I'm Diyanah.
>>> > Currently I've been working on my final year project (Offline Signature
>>> > Verification System). I'm required to use R programming and I've found that
>>> > EBImage going well with R in image processing. I've successfully install R
>>> > and EBImage package (along with ImageMagick and GTK). The thing is, when I
>>> > try the command that I get from the "Introduction to EBImage" manual, I
>>> > receive error/warning message. I hope you may help me solving these problem.
>>> >
>>> >
>>> > I have already change the directory to where the image is placed, and I
>>> > have confirmed it by calling a .txt file and it is a success, but when I try
>>> > for the image, I received these:
>>> >
>>> >  -- output of sessionInfo():
>>> >
>>> > > f =system.file("Images","user186g1.tif", pakage="EBImage")
>>>
>>> You spelled 'package' wrong.
>
> I'm not sure what version of R or EBImage you are using, but in the
> current release version of EBImage, there is no file "user186g1.tif"
> anywhere in the package. What the above command does is look inside
> the installed package for a file. Perhaps you want to manipulate a
> file you have created? If so, you don't want to use system.file() but
> instead point to the directory where you created the file.
> Sounds like you are already in the right directory, so what happens if
> you just do this:
>
>  f =system.file("user186g1.tif")
> user186g1 = readImage (f)
>

Sorry, typo, I meant to say:

user186g1 = readImage("user186g1.tif")

Dan



> ?
>
>>>
>>> > > user186g1 = readImage (f)
>>> > Warning message:
>>> > In readImage(f) : requested image not found or could not be loaded
>>> >
>>> >
>>> > I try calling the directory by the using the PATH (I'm not sure whether
>>> > the command is correct):
>>> >
>>> >
>>> > > f =system.file("D:\\FYP ~\\image","user186g1.tif", pakage="EBImage")
>>>
>
> This is now how you set or get the PATH environment variable. In any
> case that is not what you want to do, I think; use
>
> getwd()
> to find out what directory you are in.
> and
> setwd()
> to change directories.
>
> Dan
>
>
>>> Misspelled 'package' again.
>>> Dan
>>>
>>> > > user186g1 = readImage(f)
>>> > Warning message:
>>> > In readImage(f) : requested image not found or could not be loaded
>>> >
>>> > --
>>> > Sent via the guest posting facility at bioconductor.org.
>>> >
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>>
>>
>>
>>
>> --
>> Nurdiyanah Bt Hj Jambari
>> Student
>> Faculty of Engineering
>> Bachelor Engineering of Computer & Communication System Engineering
>> University Putra Malaysia