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Sequence aquisition

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Brian Ashcroft

Sequence aquisition

I am trying to figure out how to collect 100 images in burst mode. I am using the python wrapper and have tried the following steps.

mmc.startSequenceAcquisition(100,100,False)
while(mmc.isSequenceRunning()):
pass

for i in range(100):
img = mmc.popNextImage()
print img

This fails after about 20 images

getLastImage only seems to return the last image collected, so the sequence is worthless. How do you set it up to collect a sequence of 100 images. If I dont wait for the sequence to finish, i.e. collect the images as they are being aquired, then i just get a static image.

Thank you

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Arthur D. Edelstein

Re: Sequence aquisition

Hi Brian,

Maybe you need to increase the size of the circular buffer? You can use the function setCircularBufferMemoryFootprint(megabytes) .

Arthur

On Fri, Oct 21, 2011 at 12:45 PM, Brian Ashcroft <[hidden email]> wrote:

I am trying to figure out how to collect 100 images in burst mode. I am using the python wrapper and have tried the following steps.

mmc.startSequenceAcquisition(100,100,False)
while(mmc.isSequenceRunning()):
pass

for i in range(100):
img = mmc.popNextImage()
print img

This fails after about 20 images

getLastImage only seems to return the last image collected, so the sequence is worthless. How do you set it up to collect a sequence of 100 images. If I dont wait for the sequence to finish, i.e. collect the images as they are being aquired, then i just get a static image.

Thank you

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
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http://p.sf.net/sfu/cisco-dev2dev
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Nico Stuurman-4

Re: Sequence aquisition

In reply to this post by Brian Ashcroft

On Oct 21, 2011, at 12:45 PM, Brian Ashcroft wrote:

I am trying to figure out how to collect 100 images in burst mode. How do you set it up to collect a sequence of 100 images. If I dont wait for the sequence to finish, i.e. collect the images as they are being aquired, then i just get a static image.

See:

https://valelab.ucsf.edu/svn/micromanager2/branches/micromanager1.3/mmstudio/src/org/micromanager/fastacq/DiskStreamingThread.java

for an example. The most relevant code is the following:

 while ((core_.getRemainingImageCount() > 0 || core_.isSequenceRunning()) && !error && !stop_)
         {
            if (core_.getRemainingImageCount() > 0)
            {
               long start = GregorianCalendar.getInstance().getTimeInMillis();
               Object img = core_.popNextImage();
               double interval = core_.getBufferIntervalMs();
               if (stack_) {
                  ip.setPixels(img);
                  stack.addSlice(Integer.toString(stack.getSize()+1), ip);
                  acqData_.insertImageMetadata(count, 0, 0);                  
               } else {
                  acqData_.insertImage(img, count, 0, 0);                  
               }
               acqData_.setImageValue(count, 0, 0, ImagePropertyKeys.EXPOSURE_MS, expMs);
               
            } else {
               // wait for next image
               //gui_.displayStreamingMessage("Waiting...");
               Thread.sleep(100);
            }
         }

Thank you

------------------------------------------------------------------------------
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demand for specialized networking skills is growing even more rapidly.
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Brian Ashcroft

Re: Sequence aquisition

In reply to this post by Arthur D. Edelstein

So I have tried to set up a bigger buffer, so I am not getting any errors thrown, but all I get is 100 black images. Is there something big that I am missing?

from pylab import *
ion()
import MMCorePy
mmc = MMCorePy.CMMCore()
mmc.loadDevice("cam","DemoCamera","DCam")
mmc.initializeDevice("cam")
print "Test acquire and display of monochrome images."
figure()
mmc.setCameraDevice("cam")
mmc.snapImage()
im1 = mmc.getImage()
imshow(im1,cmap = cm.gray)
width=mmc.getImageWidth()
height=mmc.getImageHeight()
BufferSize=width*height*2*100/1048576
mmc.setCircularBufferMemoryFootprint(BufferSize)
mmc.startSequenceAcquisition(100,100,False)
while(mmc.isSequenceRunning()):
pass
for i in range(100):
img = mmc.popNextImage()
imshow(im1,cmap = cm.gray)

________________________________

From: Arthur D. Edelstein [mailto:[hidden email]]
Sent: Fri 10/21/2011 1:18 PM
To: Micro-Manager General
Subject: Re: [micro-manager-general] Sequence aquisition

Hi Brian,

Maybe you need to increase the size of the circular buffer? You can use the function setCircularBufferMemoryFootprint(megabytes) .

Arthur

On Fri, Oct 21, 2011 at 12:45 PM, Brian Ashcroft <[hidden email]> wrote:

I am trying to figure out how to collect 100 images in burst mode. I am using the python wrapper and have tried the following steps.

mmc.startSequenceAcquisition(100,100,False)
while(mmc.isSequenceRunning()):
pass

for i in range(100):
img = mmc.popNextImage()
print img

This fails after about 20 images

getLastImage only seems to return the last image collected, so the sequence is worthless. How do you set it up to collect a sequence of 100 images. If I dont wait for the sequence to finish, i.e. collect the images as they are being aquired, then i just get a static image.

Thank you

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
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about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
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Brian Ashcroft

Re: Sequence aquisition

In reply to this post by Arthur D. Edelstein

My bad. Just totally screwed up something unrelated and now it works great.

Brian

________________________________

From: Arthur D. Edelstein [mailto:[hidden email]]
Sent: Fri 10/21/2011 1:18 PM
To: Micro-Manager General
Subject: Re: [micro-manager-general] Sequence aquisition

Hi Brian,

Maybe you need to increase the size of the circular buffer? You can use the function setCircularBufferMemoryFootprint(megabytes) .

Arthur

On Fri, Oct 21, 2011 at 12:45 PM, Brian Ashcroft <[hidden email]> wrote:

I am trying to figure out how to collect 100 images in burst mode. I am using the python wrapper and have tried the following steps.

mmc.startSequenceAcquisition(100,100,False)
while(mmc.isSequenceRunning()):
pass

for i in range(100):
img = mmc.popNextImage()
print img

This fails after about 20 images

getLastImage only seems to return the last image collected, so the sequence is worthless. How do you set it up to collect a sequence of 100 images. If I dont wait for the sequence to finish, i.e. collect the images as they are being aquired, then i just get a static image.

Thank you

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

------------------------------------------------------------------------------
The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

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