Openslide input support about iipsrv

[geektortoise]

2 years later ...

To compile our branch of iipsrv, you can follow our Dockerfile.

I tried some month ago to rebase our branch on the master but

• A first (and huge) problem was the format detection. Our code here doesn't work with the new detection because a lot of format (as ndpi) have the same magic number than TIFF ( magic number)
• A second problem was than the new rebased branch was slow with my modifications. But I think the problem was on my side :-)

So, the first problem to solve will be a efficient format detection between TIFF and "proprietary near TIFF format". :/

[boskar]

https://github.com/cytomine/iipsrv seems to implement this feature, although it does not compile for me - configure scripts does not include openslide.h

EDIT:
/usr/local/ was hardcoded for include, after fixing it I've managed to compile it, but It does not work.

<----------------------------------->
Sat Jun 14 12:08:02 2014

IIPImage Server. Version 1.0
*** Ruven Pillay <[email protected]> ***

Verbosity level set to 2
Running in FCGI mode

Setting maximum image cache size to 10MB
Setting filesystem prefix to ''
Setting default JPEG quality to 90
Setting maximum CVT size to 5000
Setting 3D file sequence name pattern to '_pyr_'
Memcached support enabled. Connected to servers: 'localhost' with timeout 86400


Initialisation Complete.
<----------------------------------->

CVT maximum viewport size set to 5000
Full Request is FIF=<cut>&WID=150&CVT=jpeg
[1/3]: Command / Argument is FIF : <cut> (valid mrxs file)
FIF :: Image cache initialisation
FIF :: OpenSlide image requested
OpenSlideImage :: loadImageInfo()
dimensions :-1 x -1
Create virtual layer : 2147483647x2147483647
Create virtual layer : 1073741823x1073741823
Create virtual layer : 536870911x536870911
Create virtual layer : 268435455x268435455
Create virtual layer : 134217727x134217727
Create virtual layer : 67108863x67108863
Create virtual layer : 33554431x33554431
Create virtual layer : 16777215x16777215
Create virtual layer : 8388607x8388607
Create virtual layer : 4194303x4194303
Create virtual layer : 2097151x2097151
Create virtual layer : 1048575x1048575
Create virtual layer : 524287x524287
Create virtual layer : 262143x262143
Create virtual layer : 131071x131071
Create virtual layer : 65535x65535
Create virtual layer : 32767x32767
Create virtual layer : 16383x16383
Create virtual layer : 8191x8191
Create virtual layer : 4095x4095
Create virtual layer : 2047x2047
Create virtual layer : 1023x1023
Create virtual layer : 511x511
Create virtual layer : 255x255
image_widths[0]4294967295
image_heights[0]4294967295
image_widths[1]2147483647
image_heights[1]2147483647
image_widths[2]1073741823
image_heights[2]1073741823
image_widths[3]536870911
image_heights[3]536870911
image_widths[4]268435455
image_heights[4]268435455
image_widths[5]134217727
image_heights[5]134217727
image_widths[6]67108863
image_heights[6]67108863
image_widths[7]33554431
image_heights[7]33554431
image_widths[8]16777215
image_heights[8]16777215
image_widths[9]8388607
image_heights[9]8388607
image_widths[10]4194303
image_heights[10]4194303
image_widths[11]2097151
image_heights[11]2097151
image_widths[12]1048575
image_heights[12]1048575
image_widths[13]524287
image_heights[13]524287
image_widths[14]262143
image_heights[14]262143
image_widths[15]131071
image_heights[15]131071
image_widths[16]65535
image_heights[16]65535
image_widths[17]32767
image_heights[17]32767
image_widths[18]16383
image_heights[18]16383
image_widths[19]8191
image_heights[19]8191
image_widths[20]4095
image_heights[20]4095
image_widths[21]2047
image_heights[21]2047
image_widths[22]1023
image_heights[22]1023
image_widths[23]511
image_heights[23]511
image_widths[24]255
image_heights[24]255
OpenSlide :: openImage() :: 411 microseconds
FIF :: Image dimensions are 4294967295 x 4294967295
FIF :: Image contains 3 channels with 8 bits per pixel
FIF :: Image timestamp: Tue, 04 Mar 2014 14:03:01 GMT
FIF :: Total command time 493 microseconds
[2/3]: Command / Argument is WID : 150
WID handler reached
[3/3]: Command / Argument is CVT : jpeg
CVT handler reached
<----------------------------------->
Sat Jun 14 12:08:07 2014 (reinitialisation)

Are mrxs files supported, @cytomine ?

[ruven]

Looking at this explanation, it looks like ndpi is still mostly a standard TIFF, but with extra headers that make libtiff reject it. Perhaps, therefore, some secondary testing code could be added to allow iipsrv to pass a file rejected by libtiff to a second codec, such as openslide.

How about the other formats? Are any of them identifiable through a file magic number?