I am trying to run ADNI .mnc image in MATLAB
I added folder emma-master, niak-0.7.1-ammo, mia and niak-0.7.1-ammo to my path. All these folders are located in
D:\EMINA BURCH\PhD Thesis\MATLAB Packages
But when I want to open ._bq_t_15T.mnc located also in D:\EMINA BURCH\PhD Thesis\MATLAB Packages
that is h = openimage('._bq_n_15T.mnc')
I get the following error
Error using miinquire (line 145)
Error getting image dimensions from file D:\EMINA BURCH\PhD Thesis\MATLAB Packages._bq_n_15T.mnc
Error in openimage (line 173)
DimSizes = miinquire (filename, 'imagesize');
When I enter debug mode in minquire function after the line
[stat,out] = system(['mincinfo -vardims image ' minc_file]);
I get stat = 1 and out = 'mincinfo' is not recognized as an internal or external command, operable program or batch file.
May You, please help me with this issue.
system isn't able to automatically recognise the different requirements that might be needed to run the same system command on different operating systems. Using commands like ispc, isunix, ismac and computer, you can automatically check and call different versions of the commands as appropriate:
if ispc
[stat,out] = system(['mincinfo.exe -vardims image ' minc_file]);
else
[stat,out] = system(['mincinfo -vardims image ' minc_file]);
end
Of course, you also have to have the appropriate program on your MATLAB path for this to work.
Related
After booting SWUpdate yocto-generated image for the first time, executing swupdate results in error message:
Error parsing configuration file: 'globals' section missing, exiting.
I tried to strictly follow SWUpdate's documentation, but it gets short when it comes to yocto integration. I'm using meta-swupdate, meta-swupdate-boards, and meta-openembedded layers together with poky example repository all at Kirkstone tag, building via bitbake update-image and having modyfied local.conf as:
MACHINE ??= "raspberrypi4-64"
ENABLE_UART = "1"
RPI_USE_U_BOOT = "1"
IMAGE_FSTYPES = "wic ext4.gz"
PREFERRED_PROVIDER_u-boot-fw-utils = "libubootenv"
IMAGE_INSTALL:append = " swupdate"
Is there anything else I need to modify to generate the configuration file and be able to run SWUpdate binary properly?
Side question: In the documentation, it's recommended to append swupdate-www to achieve a better web server. However, if I append it, there is no swupdate-www binary inside the `/usr/bin' directory.
As with other recipes folders the recipes-support/swupdate/swupdate/raspberrypi4-64 folder was missing inside the meta-swupdate-boards layer. Therefore, an empty config file was always generated. After adding this folder and all related files, strongly inspired by raspberrypi3 folder, the error was gone and swupdate -h provided the expected output.
There was also one new error during build process thrown by yocto. It was related to missing systemd requirement and was solved by adding:
DISTRO_FEATURES_append = " systemd"
to local.conf
So the C program i am building has to be placed within the PA_mobile file on the desktop of my MAC computer (OS X 10.9.4) so it can access the scripts and text file caches that are associated with it.
now when my program launches, it validates the current working directory, comparing it to a string variable which contains the correct working directory, and requests a working directory change if the program is not located in the desktop.
here is the code associated with the directory path validation:
char* cwd_2;
char buff[PATH_MAX + 1];
cwd_2 = getcwd( buff, PATH_MAX + 1 );
char desired_working_directory[50] = "/Users/haydn/Desktop/PA_mobile";
if( cwd_2 != NULL )
{
printf("\n-----------------------------------");
printf("\nCurrent working directory: [%s]\n", cwd_2 );
usleep(10000);
printf("Desired working directory: [%s]\n",desired_working_directory);
usleep(50000);
if(strcmp(desired_working_directory, cwd_2) == 0)
{
fflush(stdout);
printf("Appropriate Working Directory achieved!\n");
printf("-----------------------------------");
}
else
{
printf("Critical Error: inapropriate working directory!\n");
printf("please relocate the 'PA_mobile' file to [/users/user/Desktop] and re-launch\n");
getchar();
exit();
}
}
The program compares the current working directory path as determined by the cwd_2 variable and compares it to the desired working directory path as described in the desired_working_directory variable.
Now here is what the program displays when run:
-----------------------------------
Current working directory: [/users/haydn/DEsktop/PA_mobile]
Desired working directory: [/Users/haydn/Desktop/PA_mobile]
Critical Error: inapropriate working directory!
please relocate file to [/users/haydn/Desktop] and re-launch
Notice that the current working directory displayed (which is determined by the getcwd( buff, PATH_MAX + 1 ); function describes the desktop file as DEsktop instead of Desktop as it is meant to be. i have checked the actual desktop folder, it is spelt without a capital E, and the capital E appears to be causing the problem, and exists solely within this code, can anyone help me?
If you run diskutil list / (or diskutil info / on latter variants of Mac OSX) you'll see whether the file system is case sensitive or not. You may need to do it on a file system lower in the hierarchy than / if those directories are in a separate file system.
You could also try the following sequence of commands:
touch /Users/haydn/Desktop/xyzzy
touch /Users/haydn/Desktop/xyzzY
ls /Users/haydn/Desktop/xyzz*
and see how many files are there. One means case-insensitive, two means case sensitive.
It's the file system personality that dictates this and, unless it mentions case sensitivity, you can assume it's not.
In which case, there is no distinction between these:
/users/haydn/DEsktop/PA_mobile
/Users/haydn/Desktop/PA_mobile
^ ^
despite the differing letters.
If you've established that this is the problem, your code should really be adjusted to handle both cases. This question (and its answers) offer ways to do this from within your code.
I am trying to read values from ".ini" file using install script Custom Action which will be installed at the target location. Below Install-script Code line doesn't read any values even the file is there at target location during installation.
Install Script Code :
GetProfString(TARGETDIR + "SampleSetup.ini","Main","AppTitle",szItemName);
Custom Action : Below is the major custom Action detail which was scheduled to be run "After InstallFinalize".
Function Name : AddDesktopShortCut (Custom Install Script Function)
Target : Synchonous(Check Exit Code)
In-Script Execution : Immediate Execution
Execution Scheduling : Always execute
Install UI Sequence :
Install Exec Sequence : After IntallFinalize
Install Exec Condition : Not Installed
Remaining Settings are the default ones.
Any help will be highly appreciated. Thanks for your Time.
If that's all of your code, how can you tell if it read the value?
I would suggest either using the debugger, or sprinkling some MessageBox calls in to see what values your program uses. In particular, ensure the ini file is where your code is looking (TARGETDIR + "SampleSetup.ini" should likely be TARGETDIR ^ "SampleSetup.ini" instead), check the return code from GetProfString, and see what szItemName is after the call.
I have a .c file compiled and would like to run via a cron job but I end up getting this error:
/bin/sh: /usr/local/bin/get1Receive.c: Permission denied.
What is causing this error and how do I fix it?
Should I be running the .c file in cron or a different compiled file?
Results from /tmp/myvars
GROUPS=()
HOME=/root
HOSTNAME=capture
HOSTTYPE=x86_64
IFS='
'
LOGNAME=root
MACHTYPE=x86_64-redhat-linux-gnu
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/bin:/bin
POSIXLY_CORRECT=y
PPID=11086
PS4='+ '
PWD=/root
SHELL=/bin/sh
SHELLOPTS=braceexpand:hashall:interactive-comments:posix
SHLVL=1
TERM=dumb
UID=0
USER=root
_=/bin/sh
Results from file get1Receive.c
file get1Receive.c
get1Receive.c: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.18, not stripped
Snippet of codes.
sprintf(queryBuf1,"SELECT ipDest, macDest,portDest, sum(totalBits) FROM dataReceive WHERE timeStampID between '%s' And '%s' GROUP BY ipDest, macDest, portDest ",buff1,buff2);
printf("\nQuery receive %s",queryBuf1);
if(mysql_query(localConn, queryBuf1))
{
//fprintf(stderr, "%s\n", mysql_error(localConn));
printf("Error in first query of select %s\n",mysql_error(localConn));
exit(1);
}
localRes1 = mysql_store_result(localConn);
int num_fields = mysql_num_fields(localRes1);
printf("\nNumf of fields : %d",num_fields);
printf("\nNof of row : %lu",mysql_num_rows(localRes1));
If the output of this command:
file get1Receive1.c
shows that file name to be a valid executable that part is very unusual, but okay.
Assuming you are using biz14 (or your real username's ) crontab try this:
use the command crontab -e to create this line in your crontab:
* * * * * set > /tmp/myvars
Wait a few minutes, go back into crontab -e and delete that entry.
Use the set command from the command line to see what variables and aliases exist.
Compare that with that you see in /tmp/myvars You have to change how your C code executes by changing the variables and aliases the cron job runs with.
If you are running the cron job in someone else's crontab, then you have a bigger problem. Check file permissions on get1Receive1.c. and the directory it lives in. That other user (the one who wons the crontab) has to have permissions set on your directory and get1Receive1.c so the job can run.
Example crontab entry:
0 10 * * 1-5 /path/to/get1Receive1.c > /tmp/outputfile
Read /tmp/outputfile to see what you got. You are using printf in your code. printf only writes to the controlling terminal. There is no controlling terminal, so redirect the printf stuff to a file.
Last effort on this problem:
Check return codes on EVERYTHING. All C functions like fread(), any db function, etc. If a return code gives a fail response ( these are different for different function calls) then report the error number the line number and function - gcc provides LINE and func. Example:
printf("error on line %d in my code %s, error message =%s\n", __LINE__, __func__, [string of error message]);
If you do not check return codes you are writing very poor C code.
CHECK return codes, please, now!
Permission wise you could have two issues.
1. The 'c' file's permissions don't allow who you are running it as to run it.
2. You are running the cron with a script which doesn't have permissions.
Here's a helpful post: How to give permission for the cron job file?
The fact that you are running a 'c' file and referring to it as a script makes me think you're using C shell and not writing it as a C language program which would need to be compiled and have the generated executable run by the cron. If you're not using gcc or have never called gcc on your 'C' script then it's not C and call it C shell to avoid confusion.
This is a cross post from Perl Monks and Mahalo answers, where I have not received a satisfactory response yet. Thanks for your time and spirit:
Why do I get this error message from perl:
Can't call method "scaleY" on an undefined value at C:/strawberry/perl +/site/lib/ Image/Seek.pm line 137?
I am getting the error in the title when calling the Image::Seek module from my script. My script is basically a rehash of the module's suggested code.
Here's the error again:
Can't call method "scaleY" on an undefined value at C:/strawberry/perl +/site/lib/ Image/Seek.pm line 137.
Here's my code:
#!/usr/local/bin/perl
use Imager;
use Image::Seek qw(loaddb add_image query_id savedb);
loaddb("haar.db");
my $img = Imager->new("photo-1.jpg")
or die Imager->errstr;
# my $img = Imager->new();
# $img->open(file => "photo-1.jpg")or die Imager->errstr;
add_image($img, 1);
savedb("haar.db");
Here's the section of the Image::Seek module causing the issue:
sub add_image_imager {
my ($img, $id) = #_;
my ($reds, $blues, $greens);
require Imager;
my $thumb = $img->scaleX(pixels => 128)->scaleY(pixels => 128);
for my $y (0..127) {
my #cols = $thumb->getscanline(y => $y);
for (#cols) {
my ($r, $g, $b) = $_->rgba;
$reds .= chr($r); $blues .= chr($b); $greens .= chr($g);
}
}
addImage($id, $reds, $greens, $blues); }
Line 137 is:
my $thumb = $img->scaleX(pixels => 128)->scaleY(pixels => 128);
If I remove
->scaleY(pixels => 128)
then line 129:
my #cols = $thumb->getscanline(y => $y);
gives me essentially the same error.
At this point I'm just trying to add one image to the database. There is an image in the directory where I'm running the script to add the image, named "photo-216.jpg". If I change the name to "photo-1.jpg" or "photo-0.jpg" and change the corresponding "add_image" and "query_id" to respectively 1 or 0, it's the same result.
I do have a database that is 385 KB big that comes from running makedb.pl below, but it is filled with null characters. I renamed this "haar.db". This is the database that gives me the error. If I recreate the haar.db file as an empty one, then the script hangs and after a couple of minutes, it give this different message:
"This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information."
If there is no "haar.db" the file still gives me the error in this post's title and unlike running makedb.pl, gives me no database named "haar.db".
By the way I get multiple examples of this post's title error also when trying to run this database filling script: http://www.drk7.jp/pub/imgseek/t/makedb.pl.txt/, which I was alluding to before. I obviously removed the .txt extension before trying it. The makedb.pl script is from this Japanese site: http://www.drk7.jp/MT/archives/001258.html.
If I run makedb.pl in a directory of 2423 scanned collectible postage stamps images, I get 362 instances of the error. The 2423 stamps is the number I have after removing the "small" thumbnail versions which I orignally thought might be causing the issue.
Could it be, that some of the images are less than 128 pixels and that is the issue? However if this is true why does the database get filled with null characters?...Unless they are not really null even though the editor I'm using, Notebook++, says they are.
Also note my images are of stamps which are only sometimes perfect squares. Otherwise, sometimes they are "landscape" sometimes "portrait". Maybe the issue is when the "landscape" scaled images get an X axis of 128 pixels and then their Y axis ends up less or much less. Could this be?
Thanks much
Update: Answer completely re-organized.
Image::Seek is not checking if
scaleX returned error. In your case, for some images, scaleX is failing.
You seem to know for which images scaleX is failing. So, leave your current
code aside, and put together a short test script:
#!/usr/bin/perl
use strict;
use warnings;
use Imager;
die "Specify image file name\n" unless #ARGV;
my ($imgfile) = #ARGV;
my $img = Imager->new;
$img->read( file => $imgfile )
or die "Cannot read '$imgfile': ", $img->errstr;
my $x_scaled = $img->scaleX( pixels => 128 )
or die 'scaleX failed: ', $img->errstr;
my $thumb = $x_scaled->scaleY( pixels => 128 )
or die 'scaleY failed: ', $x_scaled->errstr;
__END__
Running this test script, you got the error message:
Cannot read 'photo-1.jpg': format 'jpeg' not supported - formats bmp,
ico, pnm, raw, sgi, tga available for reading
indicating the underlying problem: When you installed Imager via Strawberry
Perl's cpan, the libraries for png, jpg etc were not installed. One
solution is to build those libraries with the gcc compiler provided with
Strawberry Perl.
First, you will need zlib.
C:\Temp\zlib-1.2.3> copy win32\Makefile.gcc Makefile
Set prefix = /strawberry/c/local in the Makefile. Compile. You may have to
manually copy the files zlib.h and zconf.h to
C:\strawberry\c\local\include and zlib1.dll, libz.a and libzdll.a to
C:\strawberry\c\local\lib (I don't know because I do not use Strawberry Perl very often and my Strawberry environment is very neglected.)
Then, get libpng. I used the source archive without config script.
C:\Temp\libpng-1.2.38> copy scripts\makefile.mingw Makefile
C:\Temp\libpng-1.2.38> make prefix=/strawberry/c/local ZLIBLIB=/strawberry/c/local/lib ZLIBINC=/strawberry/c/local/include
This built the PNG library. Again, you may have to manually copy the .dll,
.a and .h files to the appropriate directories. I did because of my less
than perfect Strawberry environment.
Finally, get the JPEG library.
C:\Temp\jpeg-7> copy Makefile.ansi Makefile
Make sure to edit this file and set CC=gcc. Customize jconfig.h according
to the instructions in jconfig.txt. I used jconfig.dj as a basis.
You might also want to set
CFLAGS= -O2
SYSDEPMEM= jmemansi.o
in Makefile, and
#define DEFAULT_MAX_MEM 4*1024*1024
in jconfig.h. After running make, again copy the files as needed (and as explained by install.txt).
Once the libraries are installed, you can
C:\Temp> SET IM_INCPATH=C:\strawberry\c\local\include
C:\Temp> SET IM_LIBPATH=C:\strawberry\c\local\lib
C:\Temp> cpan
cpan> force install Imager
which yields:
gif: includes not found - libraries not found
ungif: includes not found - libraries not found
jpeg: includes found - libraries found
png: includes found - libraries found
tiff: includes not found - libraries not found
freetype2: includes not found - libraries not found
freetype2: not available
T1-fonts: includes not found - libraries not found
TT-fonts: includes not found - libraries not found
w32: includes found - libraries found
If all of this is too much work, it is ... sigh I just realized the
binaries are available at GnuWin32.