I have already installed the both plugins but don't know how to use them for pod analysis. Need help in that as i don't have programming background. Also can we use it for batch processing of images, in case i have more than 100 images?
Another approach per specially coded ImageJ-macro gives reasonable estimates of the widths and lengths of all pods in the sample image. You can access the macro code from here. Unzip the zip-archive and drop the file "plantPodDimensions.ijm" onto the ImageJ main window. Then open the sample image and run the macro. The estimated pod dimensions appear in a table.
Specimen [right to left] Mean Pod Width [cm] Pod Length [cm]
OHiI7_pod-1 0.70±0.11 23.6
OHiI7_pod-2 0.59±0.09 22.3
OHiI7_pod-3 0.64±0.05 20.7
OHiI7_pod-4 0.41±0.04 20.5
OHiI7_pod-5 0.66±0.07 22.9
OHiI7_pod-6 0.68±0.10 24.4
OHiI7_pod-7 0.60±0.07 20.5
Of course it couldn't be tested, if the macro works as expected for other images than the sample image.
With the download of the plugins come documents that explain the use of the plugins. Batch processing is possible, if the starting points of the traces are known or can somehow be determined by additional pre-processing steps (not trivial). Both plugins are macro-recordable. In any case, batch processing will require some macro code.
For the use case in question I would recommend to perform the analyses via the GUI, not per batch processing. The coding of a suitable macro would take more time than the processing of 100+ images.
Related
I have a simple script that uses music21 to process the notes in a midi file:
import music21
score = music21.converter.parse('www.vgmusic.com/music/console/nintendo/nes/zanac1a.mid')
for i in score.flat.notes:
print(i.offset, i.quarterLength, i.pitch.midi)
Is there a way to also obtain a note's voicing / midi program using a flat score? Any pointers would be appreciated!
MIDI channels and programs are stored on Instrument instances, so use getContextByClass(instrument.Instrument) to find the closest Instrument in the stream, and then access its .midiProgram.
Be careful:
.midiChannel and .midiProgram are 0-indexed, so MIDI channel 10 will be 9 in music21, etc., (we're discussing changing this behavior in the next release)
Some information might be missing if you're not running the bleeding edge version (we merged a patch yesterday on this topic), so I advise pulling from git: pip install git+https://github.com/cuthbertLab/music21
.flat is going to kill you, though, if the file is multitrack. If you follow my advice you'll just get the last instrument on every track. 90% of the time people doing .flat actually want .recurse().
The following space allocation is giving me an sB37 JCL error. The cobol size of the output file is 100 bytes and the lrecl size is 100 bytes. What do you think is causing this error? I have tried increase the size to 500,100 and still get the same error.
Code:
//OUTPUT1 DD DSN=A.B.C,DISP=(NEW,CATLG,DELETE),
// DCB=(LRECL=100,BLKSIZE=,RECFM=FBM),
// SPACE=(CYL,(10,5),RLSE)
Try to increase not only the space, but the volume as well.
Include VOL=(,,,#) in your DD. # is the numbers of values you want to allocate
Ex: SPACE=(CYL,(10,5),RLSE),VOL=(,,,3) - includes 3 volumes.
Additionally, you can increase the size, but try to stay within reasonable limits :)
The documentation for B37 says the application programmer should respond as indicated for message IEC030I. The documentation for IEC030I says, in part...
Probable user error. For all cases, allocate as many units as volumes
required.
...as noted in another answer. However, be advised that the documentation for the VOL parameter of the DD statement says...
If you omit the volume count or if you specify 1 through 5, the system
allows up to five volumes; if you specify 6 through 20, the system
allows 20 volumes; if you specify a count greater than 20, the system
allows 5 plus a multiple of 15 volumes. You can override the maximum
volume count in data class by using the volume-count subparameter. The
maximum volume count for an SMS-managed mountable tape data set or a
Non-managed tape data set is 255.
...so for DASD allocations you are best served specifying a volume count greater than 5 (at least).
//OUTPUT1 DD DSN=A.B.C,DISP=(NEW,CATLG,DELETE),
// DCB=(LRECL=100,BLKSIZE=,RECFM=FBM),
// SPACE=(CYL,(10,5),RLSE)
Try this instead. Notice that the secondary will take advantage of a large dataset whereas without that parameter the largest secondary that makes any sense is < 300. Oh, and if indeed it is from a COBOL program make sure that the FD says "BLOCK 0"!!!!! If it isn't "BLOCK 0" then you might not even need to change your JCL because it wasn't fixed block machine. It was merely fixed and unblocked so the space would almost never be enough. And finally you may wish to revisit why you have the M in the RECFM to begin with. Notice also that I took out the LRECL, the BLKSIZE and the RECFM. That is because the FD in the COBOL program is all you need and putting it in the JCL is not only redundant but dangerous because any change will have to be now done in multiple places.
//OUTPUT1 DD DSN=A.B.C,DISP=(NEW,CATLG,DELETE),
// DSNTYPE=LARGE,UNIT=(SYSALLDA,59),
// SPACE=(CYL,(10,1000),RLSE)
There is a limit of 65,535 tracks per one volume. So if you will specify a SPACE that exceeds that limit - system will simply ignore it.
You can increase this limit to 16,777,215 tracks by adding DSNTYPE=LARGE paramter.
Or you can specify that your dataset is a multi volume by adding VOL=(,,,3)
You can also use DATACLAS=xxxx paramter here, however first of all you need to find it. Easy way is to contact your local Storage Team and ask for one. Or If you are familiar with ISPF navigation, you can enter ISMF;4 command to open a panel
use bellow paramters before hitting enter.
CDS Name . . . . . . 'ACTIVE'
Data Class Name . . *
It should produce a list of all available data classes. Find the one that suits you ( has enougth amount of volume count, does not limit primary and secondary space
I have a quick question about the details of running a model in JAGS and BUGS.
Say I run a model with n.burnin=5000, n.iter=5000 and thin=2. Does this mean that the program will:
Run 5,000 iterations, and discard results; and then
Run another 10,000 iterations, only keeping every second result?
If I save these simulations as a CODA object, are all 10,000 saved, or only the thinned 5,000? I'm just trying to understand which set of iterations are used to make the ACF plot?
With JAGS, n.burnin=5000, n.iter=5000 and thin=2, means you keep nothing. You run 5000, discard the first 5000 of these 5000 and then only keep a half of the remaining values of the chain (keep 1 value and discard the next one ..).
Use for example n.burnin=2000, n.iter=7000, thin=50, n.chains=5 : so you have (7000-2000)/50 * 5 = 500 values.
Could you be more specific which software you're talking about? It looks like you're referring to the arguments of the function bugs() in the R2WinBUGS package (except that the argument is called n.thin not thin). Looking at help(bugs) it just says n.burnin is the "number of iterations to discard at the beginning". Which doesn't specifically answer your question, but looking at the source for bugs.script() in that package suggests to me that it would run 5000 iterations burn in, as you suspected. You could send a suggestion to the maintainers of that package to clarify their documentation.
In your example, bugs() would then run 0 further iterations after the burn-in. Here the documentation is clearer - n.iter is the total number of iterations including the burn-in.
For your second question, the CODA output from WinBUGS (and any software which calls WinBUGS or OpenBUGS) will only include the thinned sample.
I have a 2giga mpeg file of people runnig,jogging,walking etc. in it. I will use it in a image classification project but I need to segmentate the video depending on per person an per action.
for example;
there are 25 people in video which repeat these actions in order
1st person
-runs
-walks
2nd person
-runs
-walks
and goes on....
and what I want is to have 2 different mpeg file for each person
such as;
firstperson_runs.mpeg
firstperson_waves.mpeg
so I need a tool to split big file into these files. Splitting shall be due to time.
such as;
pick t1:start of action
pick t2:end of action
create a new video from big file for the interval t1 and t2
of course I will select time intervals for each video.
OS:Winxp pro
if it can be done by matlab ,can you describe it?
any help???
I imagine there are a number of tools available to do this without MATLAB, but if you really want to use MATLAB I would check out these submissions on The MathWorks File Exchange:
Gerald Dalley's videoIO Toolbox for Matlab
Micah Richert's mmread
David Foti's mpgread and mpgwrite
EDIT:
As mentioned by M456, you can also use the built-in function MMREADER for creating a multimedia reader object for your movie file (and subsequently reading selected movie frames from it with the READ method). However, I don't know which version of MATLAB this function was introduced in. It is in versions 7.7 and 7.8 (R2008b and R2009a, respectively), but it is not in version 7.1.
Matlab can do such video split operations. There are two built in functions (aviread and mmreader) for reading video files. Both will create objects which contain the individual frames of the video. You can save these as separate frames or make a new video out of by using avifile.
I'm not sure if memory is the culprit here. I am trying to instantiate a GD image from data in memory (it previously came from a database). I try a call like this:
my $image = GD::Image->new($image_data);
$image comes back as undef. The POD for GD says that the constructor will return undef for cases of insufficient memory, so that's why I suspect memory.
The image data is in PNG format. The same thing happens if I call newFromPngData.
This works for very small images, like under 30K. However, slightly larger images, like ~70K will cause the problem. I wouldn't think that a 70K image should cause these problems, even after it is deflated.
This script is running under CGI through Apache 2.0, on OS 10.4, if that matters at all.
Are there any memory limitations imposed by Apache by default? Can they be increased?
Thanks for any insight!
EDIT: For clarification, the GD::Image object never gets created, so clearing out the $image_data from memory isn't really an option.
GD library eats many bytes per byte of image size. It's a well over a 10:1 ratio!
When a user uploads an image to our system, we start by checking the file size before loading it into a GD image. If it's over a threshold (1 Megabyte) we don't use it but instead report an error to the user.
If we really cared we could dump it to disk, use the command line "convert" tool to rescale it to a sane size, then load the output into the GD library and remove the temporary file.
convert -define jpeg:size=800x800 tmpfile.jpg -thumbnail '800x800' -
Will scale the image so it fits within an 800 x 800 square. It's longest edge is now 800px which should safely load. The above command will send the shrunk .jpg to STDOUT. The size= option should tell convert not to bother holding the huge image in memory, but just enough to scale to 800x800.
I've run into the same problem a few times.
One of my solutions was simply to increase the amount of memory available to my scripts. The other was to clear the buffer:
Original Script:
$src_img = imagecreatefromstring($userfile2);
imagecopyresampled($dst_img,$src_img,0,0,0,0,$thumb_width,$thumb_height,$origw,$origh);
Edited Script:
$src_img = imagecreatefromstring($userfile2);
imagecopyresampled($dst_img,$src_img,0,0,0,0,$thumb_width,$thumb_height,$origw,$origh);
imagedestroy($src_img);
By clearing out the memory of the first src_image, it freed up enough to handle more processing.