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Hi Guilhem,
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<div class="">although the error message is not fully indicative, you are most certainly hitting</div>
<div class="">the limit of the Java byte array which is the type returned by the openBytes</div>
<div class="">method [1].</div>
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</div>
<div class="">Generally when working with large XY planes, you will need to read images in tiles</div>
<div class="">rather than retrieving the whole plane. To do so, you can use the signatures of</div>
<div class="">the openBytes API allowing to pass the coordinates and the dimensions of the tile</div>
<div class="">to retrieve [2].</div>
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</div>
<div class="">In the MATLAB toolbox, these coordinates and dimensions can be passed to the</div>
<div class=""> bfGetPlane function e.g. to retrieve the first 1024x1024 tile:</div>
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</div>
<div class="">r = bfGetReader(file);</div>
<div class="">I = bfGetPlane(r, 1, 1, 1, 1024, 1024);</div>
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<div class="">Best regards</div>
<div class="">Sebastien</div>
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</div>
<div class="">[1] <a href="https://downloads.openmicroscopy.org/bio-formats/5.7.3/api/loci/formats/IFormatReader.html#openBytes-int-" class="">https://downloads.openmicroscopy.org/bio-formats/5.7.3/api/loci/formats/IFormatReader.html#openBytes-int-</a> </div>
<div class="">[2] <a href="https://downloads.openmicroscopy.org/bio-formats/5.7.3/api/loci/formats/IFormatReader.html#openBytes-int-int-int-int-int-" class="">
https://downloads.openmicroscopy.org/bio-formats/5.7.3/api/loci/formats/IFormatReader.html#openBytes-int-int-int-int-int-</a></div>
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<blockquote type="cite" class="">
<div class="">On 10 Jan 2018, at 15:56, Guilhem Chenon <<a href="mailto:guilhem.chenon@espci.fr" class="">guilhem.chenon@espci.fr</a>> wrote:</div>
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<p class="">Hello,</p>
<p class="">I could not find any report of this issue online so I have to ask it here. Thanks in advance for your help.</p>
<p class="">So I have Bio-formats 5.7.2 installed on both Matlab R2017b with 7000MB of Java Heap space (with bfmatlab folder) and ImageJ (with .jar package). What I want to do is open an ND2 file (20112x20173 ; 16-bit resolution) of 11,2 Gb (12 111 798 272
bytes). It consists of 6 timepoints each containing 3 channels. So the "time points" (consisting of 3 channels and encoded as series by the Nikon Software (NIS-Elements)), are each over 2*10^9 bytes.
<br class="">
</p>
<p class="">Here is an example code:<br class="">
</p>
<p class="">[file,path] = uigetfile('*.nd2','Select .nd2 file'); <br class="">
cd(fileparts(path));<br class="">
r = bfGetReader(file);<br class="">
I = bfGetPlane(r, 1);<br class="">
</p>
<p class="">which gives, with the file cited above, the following error (same with ImageJ and Icy which all rely on LOCI) :<br class="">
</p>
<p class=""><i class="">Error using bfGetPlane (line 78)</i><i class=""><br class="">
</i><i class="">Java exception occurred:</i><i class=""><br class="">
</i><i class="">java.lang.NegativeArraySizeException</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.in.NativeND2Reader.openBytes(NativeND2Reader.java:298)</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.ImageReader.openBytes(ImageReader.java:457)</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:227)</i><i class=""><br class="">
</i><i class=""><br class="">
</i><i class=""> at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)</i></p>
<p class="">I tried to open this .nd2 with as much as 30Gb of memory in the last version of ImageJ with no success, so I does not think it has anything to do with available RAM.<br class="">
<i class=""></i></p>
<p class="">The onl<i class="">y way</i> I know to prevent the error is to use "crop on import" with Bio-formats plugin in ImageJ. I can open one serie if it's cropped to around 18800x18800px because I think it gets under the 2 Gb limit.<br class="">
<i class=""></i></p>
<p class="">So what i want to know is if there exist a workaround or do I have to crop/bin my files? If requested I can upload the file through FTP.<br class="">
</p>
<p class="">Thank you very much for your time and your help. I hope I explained myself clearly.<br class="">
</p>
<p class="">Best regards,<br class="">
</p>
<div class="moz-signature">-- <br class="">
Guilhem CHENON <br class="">
LCMD - ESPCI Paris</div>
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