README

# IIPImage forked by Cytomine

> IIPImage is an advanced high-performance feature-rich image server system for web-based streamed viewing and zooming of ultra high-resolution
  images. 

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## About

IIPImage is designed to be fast and bandwidth-efficient with low processor and memory requirements. The system can comfortably handle gigapixel size images as
well as advanced image features such as 8, 16 and 32 bits per channel, CIELAB colorimetric images and scientific imagery such as multispectral images, image sequences and 3D surface topologies.

See https://github.com/ruven/iipsrv for the official version.

This fork was made to add support for the OpenSlide library (http://openslide.org/).
By this way, iipsrv natively supports more image formats as ndpi, mrax, svs, etc.
Also, we added a custom color mapping mechanism and the possibility to export regions
of images in TIFF, with the initial bit depth.

## Features

* Fast lightweight embeddable FastCGI server module
* High performance with inbuilt configurable cache
* Support for gigapixel images
* Dynamic JPEG, PNG and TIFF export of whole or regions of images at any resolution
* Supports IIP, Zoomify, DeepZoom and IIIF protocols
* 1, 8, 16 and 32 bit image support including 32 bit floating point support
* CIELAB support with automatic CIELAB->sRGB colour space conversion
* JPEG2000 support
* Multispectral image support
* Dynamic watermarking
* Memcached support
* 3D panoramic views
* Dynamic hillshading of 3D surface topologies
* Dynamic decoder module capability
* Openslide support
* Custom color mapping

## Documentation
Detailed class descriptions (generated using doxygen) are available in the
doc subdirectory

### IIP Protocol

#### Input
Must be the fist command.

| Command | Usage | Description |
| ------- | ----| ---- |
| FIF | FIF=/path/image.tif | |
| Zoomify | Zoomify=/path/image.tif | |
| Deepzoom | DeepZoom=/path/image.tif.dzi | |

#### Output
Must be the last command.

| Command | Usage | Description |
| ------- | ----| ---- |
| CVT | `CVT=f` | Return the full image or a region, in `f` format, only `jpeg`, `png`, `tiff` supported.  |
| JTL | `JTL=r,n` | Return a tile with index `n` at resolution level `r`, in JPEG format |
| PFL | `PFL=r:x1,y1-x2,y2` | Export profile at resolution `r` from position `(x1,y1)` to `(x2,y2)`. Only horizontal or vertical profiles are currently supported |
| SPECTRA | `SPECTRA=r,t,x,y` | Return pixel values in all image channels for a particular point `(x,y)` on tile `t` at resolution `r` in XML format. |

#### Transformation parameters
| Command | Usage | Description |
| ------- | ----| ---- |
| WID | `WID=w` | Requested export image width `w` in pixels for CVT requests |
| HEI | `HEI=h` | Requested export image height `h` in pixels for CVT requests |
| RGN | `RGN=x,y,w,h` | Define a region of interest starting at relative coordinates `(x,y)` with width `w` and height `h`. All values should be in ratios 0-1.0  |
| CNT | `CNT=c` | Contrast – multiplication of pixel values by factor `c`|
| GAM | `GAM=g` | Apply gamma correction `g`|
| CMP | `CMP=s` | Generate colormap using one of the colormap schemes `s`, pre-defined `red`, `green`, `blue`, `hot`, `cold`, `jet`, or customized `/path/colormap.cmap`  |
| INV | `INV` | Invert image or colormap |
| ROT | `ROT=r` | Rotate the image by `r`|
| QLT | `QLT=q` | JPEG quality factor `q` between 0 (worst) and 100 (best) |
| MINMAX | `MINMAX=c:min,max` | Set minimum `min` and maximum `max` for channel `c`|
| BIT | `BIT=b` | Output bit depth `b` (8 for JPEG, 8/16 for PNG, 8/16/32 for TIFF) |




## License

iipsrv is released under the GNU General Public License (GPL). See the copyright
notice COPYING in this directory for licensing details or go to
http://www.gnu.org/licenses/gpl.html for more details.

If you use IIPImage on a public site and remove the IIP link logo from the 
client, you must provide a link on your site back to the IIPImage site - 
http://iipimage.sf.net

This distribution includes version 2.4.0 of the FCGI development libraries.
See COPYING.FCGI for licensing information for these libraries.



## Requirements
Requirements: openslide, libtiff, zlib and the IJG JPEG development libraries.
Optional: libmemcached (for Memcached) and Kakadu or OpenJPEG (for JPEG2000).

Plus, of course, an fcgi-enabled web server. The server has been successfully
tested on the following servers:
- [Apache](https://httpd.apache.org)
- [Lighttpd](https://www.lighttpd.net)
- [IIS](https://www.iis.net)
- [NginX](https://nginx.org)
- [MyServer](http://www.myserverproject.net)
- Java Application Servers (Tomcat, JBoss)

Example server configurations are shown below.



## Building
The standard autoconf build process should work fine. If you want to allow
dynamic loading of 3rd party image decoders, use the configure option
--enable-modules. There is a version of the FCGI development library included
in this distribution. The configure script will use this bundled version
unless it detects one already installed. Alternatively, you may specify the
path using --with-fcgi-incl=<path> and --with-fcgi-lib=<path>.

If this is an SVN or Git development version, first generate the autoconfigure
environment using autogen.sh:

    ./autogen.sh

Otherwise for release versions, use configure directly:

    ./configure
    make


### OPTIONAL LIBRARIES: MEMCACHED
IIPImage is able to use Memcached (http://www.memcached.org), a high-performance,
distributed memory object caching system. If enabled, IIPImage will cache
results using Memcached, giving IIPImage added speed and scalability. To use
this, you will need to install the library (and development files) of
libmemcached (http://libmemcached.org). This will be automatically detected
during the build process. 



### OPTIONAL LIBRARIES: KAKADU
IIPImage is able to decode JPEG2000 images via the Kakadu SDK
(http://www.kakadusoftware.com). This is, however, not open source and you will
need to purchase a license for the source code. In order to use, first build
the Kakadu SDK as per the instructions supplied with the SDK. Then, supply the
following parameters to the ./configure command

    --with-kakadu=/path/to/kakadu/distribution



### OPTIONAL LIBRARIES: OPENJPEG
IIPImage is able to decode JPEG2000 images via the open source OpenJPEG 
library (http://www.openjpeg.org/). Activated if OpenJPEG development
files found in system path or path provided via

    --with-openjpeg=/path/to/openjpeg/distribution

OpenJPEG will be disabled if Kakadu support has been requested or --disable-openjpeg used.



## INSTALLATION
Simply copy the executable called iipsrv.fcgi in the src subdirectory into
the web server fcgi directory. If one does not exist, simply create one, called,
for example, fcgi-bin. The web server will need to be configured to use this
executable.



## CONFIGURATION
There are several startup variables that can be passed to the server.
They are all optional.

LOGFILE: the server will log its output to the file specified, if it can.
Version 1.1 and later of iipsrv also supports logging to syslog if “syslog”
is given as the value.

VERBOSITY: 0 means no logging, 1 is minimal logging, 2 lots of debugging stuff,
3 even more debugging stuff and 10 a very large amount indeed ;-)

MAX_IMAGE_CACHE_SIZE: Max image cache size to be held in RAM in MB. This is
a cache of the compressed JPEG image tiles requested by the client.
The default is 10MB.

FILESYSTEM_PREFIX: This is a prefix automatically added by the server to the 
beginning of each file system path. This can be useful for security reasons to 
limit access to certain sub-directories. For example, with a prefix of 
"/home/images/" set on the server, a request by a client for "image.tif" will 
point to the path "/home/images/image.tif".  Any reverse directory path 
component such as ../ is also filtered out. No default value.

JPEG_QUALITY: The default JPEG quality factor for compression when the
client does not specify one . The value should be between 1 (highest level of
compression) and 100 (highest image quality). The default is 75.

MAX_CVT: Limits the maximum image dimensions in pixels (the WID or HEI 
commands) allowable for dynamic JPEG export via the CVT command. This 
prevents huge requests from overloading the server. The default is 5000.

ALLOW_UPSCALING: Determines whether an image may be rendered at a size greater
than that of the source image. A value of 0 will prevent upscaling.
The default is 1 (upscaling is allowed).

MAX_LAYERS: The maximum number of quality layers to decode for images that support 
progressive quality encoding, such as JPEG2000. Ignored for other file 
formats. If not set, half of the available quality layers will be decoded by default.
If set to -1, all the available layers will be decoded by default.

FILENAME_PATTERN: Pattern that follows the name stem for a 3D or multispectral 
sequence. eg: "_pyr_" for FZ1_pyr_000_090.tif. The default is "_pyr_". This is 
only relevant to 3D image sequences.

WATERMARK: TIFF image to use as watermark file. This image should be not be 
bigger the tile size used for TIFF tiling. If bigger, it will simply be 
cropped to the tile size. If smaller, the watermark will be positioned 
randomly within the available space. The image can be either colour or 
grayscale.

WATERMARK_PROBABILITY: The probability that a particular tile will have a watermark
applied to it. 0 means never, 1 means always.

WATERMARK_OPACITY: The opacity (between 0 and 1) applied to the watermark image.

MEMCACHED_SERVERS: A comma-delimitted list of memcached servers with optional
port numbers. For example: localhost,192.168.0.1:8888,192.168.0.2.

MEMCACHED_TIMEOUT: Time in seconds that cache remains fresh.
Default is 86400 seconds (24 hours).

INTERPOLATION: Interpolation method to use for rescaling when using image export.
Integer value. 0 for fastest nearest neighbour interpolation. 1 for bilinear
interpolation (better quality but about 2.5x slower). Bilinear by default.

CORS: Cross Origin Resource Sharing setting. Disabled by default.
Set to * to enable for all domains or specify a single domain.
See http://www.w3.org/TR/cors/ for more details on CORS.

BASE_URL: Set a base URL for use in certain protocol requests if web server rewriting 
has taken place and the public URL is not the same as that supplied to iipsrv.

URI_MAP: Set a mapping from a URL prefix to a supported protocol. This enables iipsrv to
be able to work without requring full CGI query strings. Map must be of the form
"prefix=>protocol" where prefix can be either empty or any string prefix and protocol must
be one of IIP,IIIF,DeepZoom, Zoomify. Used, for example, to map requests of the form
http://server/iiif/ to the IIIF protocol handler without requiring web server rewriting.

CACHE_CONTROL: Set the HTTP Cache-Control header. See http://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html#sec14.9 for 
a full list of options. If not set, header defaults to "max-age=86400" (24 hours).

EMBED_ICC: Set whether the ICC profile is embedded within the output image.
0 to strip profile, 1 to embed profile. The default is 1 (embedded profiles).

OMP_NUM_THREADS: Set the number of OpenMP threads to be used by the iipsrv image
processing routines (See OpenMP specification for details). All available processor
threads are used by default.

KAKADU_READMODE: Set the Kakadu JPEG2000 read-mode. 0 for 'fast' mode with minimal error checking (default), 1 for 'fussy' mode with no error
recovery, 2 for 'resilient' mode with maximum recovery from codestream errors. See the Kakadu documentation for further details.

DECODER_MODULES: Comma separated list of external modules for decoding
other image formats. This is only necessary if you have activated 
--enable-modules for ./configure and written your own image format 
handler(s).




## IMAGE PATHS
The images paths given to the server via the FIF variable must be
absolute paths on the server machine (eg. FIF=/images/test.tif) 
and not paths relative to the web server document root location.
Images do not, therefore, need to be directly accessible by the
client via the web server. Make sure the server process owner is
able to access and read the images!



## EXAMPLE SERVER CONFIGURATIONS
### Apache and mod_fastcgi

httpd.conf example extract:

```
# Create a directory for the iipsrv binary
ScriptAlias /fcgi-bin/ "/usr/local/httpd/fcgi-bin/"

# Set the options on that directory
<Directory "/usr/local/httpd/fcgi-bin">
   AllowOverride None
   Options None

# Syntax for access is different in Apache 2.4 - uncomment appropriate version
# Apache 2.2
#   Order allow,deny
#   Allow from all

# Apache 2.4
   Require all granted

</Directory>

# Set the module handler
AddHandler fastcgi-script fcg fcgi fpl

# Initialise some variables for the FCGI server
FastCgiServer /usr/local/httpd/fcgi-bin/iipsrv.fcgi \
-initial-env LOGFILE=/tmp/iipsrv.log \
-initial-env VERBOSITY=2 \
-initial-env MAX_IMAGE_CACHE_SIZE=10 \
-initial-env FILENAME_PATTERN=_pyr_ \
-initial-env JPEG_QUALITY=50 \
-initial-env MAX_CVT=3000 \
-listen-queue-depth 2048 \
-processes 1
```


### Apache and mod_fcgid

mod_fcgid is a binary compatible replacement for mod_fastcgi. It works in the 
same way, but is configured differently. Load the module like this:


    LoadModule fcgid_module /path/to/apachemodules/mod_fcgid.so


Here is an example configuration. Note that mod_fcgid does not have a 
FastCgiServer directive and there is no need to explicitly start the server:

```
# Create a directory for the iipsrv binary
ScriptAlias /fcgi-bin/ "/var/www/localhost/fcgi-bin/"

# Set the options on that directory
<Directory "/var/www/localhost/fcgi-bin/">
   AllowOverride None
   Options None

# Syntax for access is different in Apache 2.4 - uncomment appropriate version
# Apache 2.2
#   Order allow,deny
#   Allow from all

# Apache 2.4
   Require all granted

   # Set the module handler
   AddHandler fcgid-script .fcgi
</Directory>

# Set our environment variables for the IIP server
FcgidInitialEnv VERBOSITY "5"
FcgidInitialEnv LOGFILE "/tmp/iipsrv.log"
FcgidInitialEnv MAX_IMAGE_CACHE_SIZE "10"
FcgidInitialEnv JPEG_QUALITY "50"
FcgidInitialEnv MAX_CVT "3000"

# Define the idle timeout as unlimited and the number of
# processes we want
FcgidIdleTimeout 0
FcgidMaxProcessesPerClass 1
```

Note that on CentOS, FcgidIPCDir is configured by default to 
/var/log/httpd/fcgidsock, which may not be writable by Apache. If this is the case, 
specify another location for FcgidIPCDir, which is writable, such as /tmp/fcgidsock


### Lighttpd
lighttpd.conf example extract:

```
fastcgi.server = ( "/fcgi-bin/iipsrv.fcgi" =>
  (( "host" => "127.0.0.1",
     "port" => 9000,
     "check-local" => "disable",
     "min-procs" => 1,
     "max-procs" => 1,
     "bin-path" => "/var/www/localhost/fcgi-bin/iipsrv.fcgi",
     "bin-environment" => (
        "LOGFILE" => "/tmp/iipsrv.log",
        "VERBOSITY" => "5",
        "MAX_IMAGE_CACHE_SIZE" => "10",
        "FILENAME_PATTERN" => "_pyr_",
        "JPEG_QUALITY" => "50",
        "MAX_CVT" => "3000"
      )
  ))
)
```

### NginX

iipsrv can also be used with NginX. The one drawback with regards to iipsrv is that it cannot automatically spawn FCGI processes, so you will need to use 
nginx together with spawn-fcgi or start iipsrv from the command line.

To set up nginx with iipsrv add a directive such as this to your nginx configuration, which will forward requests to /fcgi-bin/iipsrv.fcgi to a 
running iipsrv process on port 9000.

```
location /fcgi-bin/iipsrv.fcgi {
	fastcgi_pass    localhost:9000;
	fastcgi_param   PATH_INFO $fastcgi_script_name;
        fastcgi_param   REQUEST_METHOD $request_method;
        fastcgi_param   QUERY_STRING $query_string;
        fastcgi_param   CONTENT_TYPE $content_type;
        fastcgi_param   CONTENT_LENGTH $content_length;
        fastcgi_param   SERVER_PROTOCOL $server_protocol;
        fastcgi_param   REQUEST_URI $request_uri;
        fastcgi_param   HTTPS $https if_not_empty;
}
```

Nginx can also handle load balancing to multiple iipsrv instances, which can be hosted on the same machine on multiple ports or on different hosts. 
For a multiple host configuration, declare the load balancing like this:

```
upstream iip {
	server 192.168.0.1:9000;
	server 192.168.0.2:9000;
	server 192.168.0.3:9000;
	server 192.168.0.4:9000;
}
```

and change the fastcgi_pass parameter in the above location configuration to point to this instead of a fixed address:

    fastcgi_pass 	iip;


### spawn-fcgi

iipsrv can also be used with lighttpd's spawn-fcgi without the need for a 
full web server. Simply spawn the iipsrv process on the command line. The 
process can be bound to an IP address and port for backend load-balancing 
configurations. For example:

    spawn-fcgi -f src/iipsrv.fcgi -a 192.168.0.1 -p 9000


### MyServer:
Simply run the MyServer configuration and in the MIME section, choose the .fcgi extension
and select:
```
MIME Type: application octet-stream
Action: Execute self contained FastCGI
Manager: NONE
```


### Java Application Servers (Tomcat, Jetty, JBoss etc)

IIPImage can also be used with Java Application Servers such as Apache Tomcat, JBoss and Jetty. Simply add 
the JFastCGI jar file to your webapp and add the following to your web.xml configuration file in order to 
re-route FCGI requests to the IIPImage server on the specified port.

```
<!-- Gateway Servlet to IIPImage FCGI server -->

<servlet>
  <servlet-name>fcgi</servlet-name>
  <servlet-class>net.jr.fastcgi.FastCGIServlet</servlet-class>
  <init-param>>
    <param-name>server-address</param-name>
   <param-value>127.0.0.1:6667</param-value>
  </init-param>
</servlet>

<servlet-mapping>
  <servlet-name>fcgi</servlet-name>
  <url-pattern>/cgi-bin/iipsrv.fcgi</url-pattern>
</servlet-mapping>
```

You then need to start an instance of the server on the requested port (6667 in this example) using 
spawn-cgi (see spawn-cgi section above) or on the command line (see below).


### Command Line

It is also possible to start iipsrv directly on the command line using the --bind parameter.
For example:

    iipsrv.fcgi --bind 192.168.0.1:9000

where the argument given to bind is the socket on which to listen to FCGI
requests. Note that these are *not* HTTP requests and iipsrv will still require a web server front-end.

There is additionally a --backlog parameter that is optional and sets the socket backlog value. The backlog value specifies the number of requests can be queued and, 
therefore, increases the number of concurrent connections that iipsrv can handle and is set to 2048 by default. For example:

    iipsrv.fcgi --bind 192.168.0.1:9000 --backlog 1024

Note that the backlog parameter must be specified after the bind parameter and argument.  Note also that this value may be limited by the operating system. On Linux kernels 
< 2.4.25 and Mac OS X, the backlog limit is hard-coded to 128, so any value above this will be limited to 128 by the OS. If you do provide a backlog value, verify whether 
the setting /proc/sys/net/core/somaxconn should be updated.

Your web server should, therefore, be configured to use this address for FastCGI.
For example with lighttpd:

    fastcgi.server = (
      "/fcgi-bin/iipsrv.fcgi" => (
            ("host"=>"192.168.0.1", "port"=>9000, "check-local"=>"disable")
      )
    )



------------------------------------------------------------------------------------
Please refer to the project site http://iipimage.sourceforge.net for further details

------------------------------------------------------------------------------------
(c) 2000-2019 Ruven Pillay <ruven@users.sourceforge.net>