[ome-users] question about Bio-Formats.
Curtis Rueden
ctrueden at wisc.edu
Wed Apr 8 20:47:26 BST 2015
Hi Qi,
> But do you know could we build a thumbnail image by our defined size
> but not use the default size?
It might work to write:
coreMeta = reader.getCoreMetadataList().get(0);
coreMeta.thumbSizeX = myDesiredSizeX;
coreMeta.thumbSizeY = myDesiredSizeY;
thumbPlane = reader.openThumbBytes(myImageNumber);
But I didn't test this. If you look at the default openThumbBytes
implementation, it is merely doing a full openBytes and then scaling the
image [1]. So you could also do it the same way in your own code. Something
like:
img = AWTImageTools.openImage(null, reader, sizeX, sizeY);
img = AWTImageTools.makeUnsigned(img);
thumb = AWTImageTools.scale(img, thumbSizeX, thumbSizeY, false);
thumbBytes = AWTImageTools.getPixelBytes(thumb, little);
Or since you like MATLAB, maybe there is a more comfortable MATLAB way for
you, such as imresize [2].
Regards,
Curtis
[1]
https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-api/src/loci/formats/FormatTools.java#L1217-L1220
[2] http://www.mathworks.com/help/images/ref/imresize.html
On Wed, Apr 8, 2015 at 1:58 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:
> Hello Curtis,
>
> Thank you very much. That is helpful. But do you know could we build a
> thumbnail image by our defined size but not use the default size? Thank you.
>
> Sincerely,
> Qi
>
> On Wed, Apr 8, 2015 at 2:46 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> Hi Qi,
>>
>> > That only only get me the size of whole image, but not the size of
>> thumbnail image.
>>
>> reader.getThumbSizeX()
>> reader.getThumbSizeY()
>>
>> Searching the Javadoc is a good way to find this stuff.
>> http://javadoc.imagej.net/Bio-Formats/loci/formats/FormatReader.html
>>
>> Regards,
>> Curtis
>>
>> On Wed, Apr 8, 2015 at 1:28 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>
>>> Hello Curtis,
>>>
>>> That only only get me the size of whole image, but not the size of
>>> thumbnail image.
>>>
>>> Sincerely,
>>> Qi
>>>
>>> On Wed, Apr 8, 2015 at 2:17 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>>
>>>> Hi Qi,
>>>>
>>>> > now I don't know the size (width and height).
>>>>
>>>> Use reader.getSizeX() and reader.getSizeY().
>>>>
>>>> -Curtis
>>>>
>>>> On Wed, Apr 8, 2015 at 1:08 PM, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>>>
>>>>> Hello Sebastien,
>>>>>
>>>>> now I just use the command
>>>>> "reader = bfGetReader('C:\000_whole_slides\tissue40x-8B.ndpi');
>>>>> plane = reader.openThumbBytes(1);"
>>>>> to get the thumbnail. But the output is a vector. 12288 x1. in the
>>>>> bfGetPlane function, you use the reshape function to transfer it to 2-D
>>>>> image. But in that function we know the size of image. And now I don't know
>>>>> the size (width and height). Do you know how to transfer it to image? Thank
>>>>> you.
>>>>>
>>>>> Sincerely,
>>>>> Qi
>>>>>
>>>>> On Wed, Apr 8, 2015 at 5:45 AM, Sebastien Besson (Staff) <
>>>>> s.besson at dundee.ac.uk> wrote:
>>>>>
>>>>>> Hi Qi,
>>>>>>
>>>>>> all understood and this certainly makes sense.
>>>>>> The Bio-Formats API has a method to return bytes corresponding to a
>>>>>> thumbnail instead of a full plane, see
>>>>>>
>>>>>> http://downloads.openmicroscopy.org/bio-formats/5.1.0/api/loci/formats/FormatReader.html#openThumbBytes(int)
>>>>>>
>>>>>> This method can be used in the same way that bfGetPlane() makes use
>>>>>> openBytes() to retrieve a single
>>>>>> plane. Here, the final array would have to be resized by the
>>>>>> thumbnail size, typically 128 x 128, instead
>>>>>> of the full plane dimensions
>>>>>>
>>>>>> Note however that the way to get thumbnails for almost all of the
>>>>>> readers is to read the pixels data
>>>>>> and scale it internally. For very large WSI, calling this method will
>>>>>> likely be restricted to the same memory
>>>>>> limitations as reading full planes.
>>>>>>
>>>>>> Best regards,
>>>>>> Sebastien
>>>>>>
>>>>>> On 7 Apr 2015, at 15:53, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>>>>>
>>>>>> Hello Sebastien,
>>>>>>
>>>>>> Thank you for your email. I am sorry, my description was not clear.
>>>>>> It is not "1-by-1". Now I could extract some sub_area of image, but the
>>>>>> extracted image is *1-to-1 *pixel with WSI. What we want is a
>>>>>> thumbnail. In other word, we want to display the whole WSI or a large part
>>>>>> of WSI in a small size. Thank you.
>>>>>>
>>>>>> Sincerely,
>>>>>> Qi
>>>>>>
>>>>>> On Mon, Apr 6, 2015 at 6:37 PM, Sebastien Besson (Staff) <
>>>>>> s.besson at dundee.ac.uk> wrote:
>>>>>>
>>>>>>> Hi Qi,
>>>>>>>
>>>>>>>
>>>>>>> Do you need a thumbnail
>>>>>>>
>>>>>>>
>>>>>>> On 6 Apr 2015, at 22:11, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>>>>>>
>>>>>>> Hello Sebastien,
>>>>>>>
>>>>>>>
>>>>>>> Hi Qi,
>>>>>>>
>>>>>>> Thank you your your reply. I think it is working.
>>>>>>>
>>>>>>>
>>>>>>> Good to hear.
>>>>>>>
>>>>>>> Now, I want to use BIO to get a WSI ( whole slide image) image.
>>>>>>> But as the WSI is to large more than 2 GB. I can't use bfopen to open it.
>>>>>>> Melissa told me a could use bfGetPlane to get the image.
>>>>>>>
>>>>>>>
>>>>>>> Indeed, if the image is large enough, reading all the planes into
>>>>>>> memory like boffin does simply does not
>>>>>>> scale and you have to read selectively.
>>>>>>>
>>>>>>> But it extract image is 1-by-1 pixel.
>>>>>>>
>>>>>>>
>>>>>>> If you have a WSI, it is surprising that the command pasted in a
>>>>>>> previous thread would return a single pixel
>>>>>>> Can you give us the full dimensions of your image as given by
>>>>>>> >> r = bfGetReader(‘\path\to\file);
>>>>>>> >> r.getSizeX()
>>>>>>> >> r.getSizeY()
>>>>>>> >> r.getSizeZ()
>>>>>>> >> r.getSizeC()
>>>>>>> >> r.getSizeT()
>>>>>>> Also, can you paste the command you use to retrieve this 1-by-1
>>>>>>> pixel array?
>>>>>>>
>>>>>>> But some time, we need and thumb image of whole image. Do you
>>>>>>> know how to extract a 1-by-N image? That means, Extract the whole image
>>>>>>> (with size 10000x10000), but only display and save in 100x100 size. Thank
>>>>>>> you.
>>>>>>>
>>>>>>>
>>>>>>> Just to be sure, do you want to read a thumbnail for the entire
>>>>>>> image? Or are you looking for a way to
>>>>>>> retrieve a tile i.e. a XY subset of the full image?
>>>>>>>
>>>>>>> Sincerely,
>>>>>>> Qi
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Sebastien
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Apr 6, 2015 at 3:26 PM, Sebastien Besson <
>>>>>>> seb.besson at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Qi,
>>>>>>>>
>>>>>>>> the content of your java.opts looks valid (although you might
>>>>>>>> want to increase the
>>>>>>>> memory settings later). According to the MATLAB documentation, e.g.
>>>>>>>>
>>>>>>>> http://uk.mathworks.com/help/matlab/matlab_env/java-opts-file.html?refresh=true
>>>>>>>> you need to put this file either in the MATLAB startup folder or
>>>>>>>> under the `bin\arch` folder
>>>>>>>> under the MATLAB root path. Locally, I have a `java.opts` under
>>>>>>>> `~/Documents/MATLAB` for
>>>>>>>> instance.
>>>>>>>>
>>>>>>>> Can you try either of these options and check the output of the
>>>>>>>> following command
>>>>>>>> >> java.lang.Runtime.getRuntime().maxMemory
>>>>>>>> reflects what it in your java.opts
>>>>>>>>
>>>>>>>>
>>>>>>>> Sebastien
>>>>>>>>
>>>>>>>> On 6 Apr 2015, at 19:53, Qi Gong <qigong at gwmail.gwu.edu> wrote:
>>>>>>>>
>>>>>>>> Hello everyone,
>>>>>>>>
>>>>>>>> Sorry for bother. I try to use Matlab version of Bio-Formats.
>>>>>>>> But I face the memory problem, I know, we could add a time named java.opts
>>>>>>>> to solve the problem.
>>>>>>>>
>>>>>>>> I put the file the java.opts into matlab folder as attachment.
>>>>>>>> But matlab still shows the warning. Could anyone help me check whether my
>>>>>>>> java.opts is correct or not? Thank you.
>>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>> Qi
>>>>>>>>
>>>>>>>>
>>>>>>>> <matlab folder.png><memory warning.png><java.opts>
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>
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