cmusatyalab / dermshare

DermShare web application and filters

Installing

Requirements

At build time

• OpenDiamond

On the web application server

• OpenDiamond

On the Diamond servers

• 64-bit environment
• OpenDiamond
• virtualenv
• OpenCV-Python
• BLAS library and headers
• LAPACK library and headers
• freetype library and headers
• libpng library and headers
• libjpeg library and headers

DermShare

1. Use make-filter.py to build the Autosegment filter.
2. Use make-filter.py to build the Gemini filter.
3. Create and populate virtualenv. Use --system-site-packages, since OpenDiamond can't be installed with pip.
4. Configure and run. dermshare.py is always needed, but dermshare-ws.py is only necessary if the mobile device link is enabled with WEBSOCKET_BASEURL.

Diamond servers

To avoid conflicts with older versions of NumPy and Six packaged by your Linux distribution, it is best to (re-)install NumPy v1.9.1 and Six v1.9.0 with pip after installing OpenCV-Python.

fil_autosegment and fil_gemini must install dependencies into a virtualenv in /tmp the first time it runs. To avoid long delays in the first search, the virtualenv can be prepopulated by running fil_autosegment and fil_gemini without arguments on the Diamond servers. To avoid additional delays whenever a Diamond server is rebooted or /tmp is cleared, you can globally install the necessary Python libraries:

pip install -r autosegment/requirements.txt
pip install -r gemini/requirements.txt

Scope server

An example scope server is provided in simplescope. The scope server shipped with OpenDiamond will not work because it doesn't integrate with Diamond web apps.

Dataretriever

An example dataretriever is provided in dataretriever. It includes support for serving segmentation images and pathology reports in addition to the Diamond objects and scope lists. The diamond_store dataretriever shipped with OpenDiamond will probably also work, but has not been tested.

Laying out the data

The DermShare dataretriever expects a directory tree with the following layout:

DERMSHARE_SCOPE_PATH
    <scope1>
        <name1>-image.{jpg|png|...}
        <name1>-segm.png
        <name1>-attr.yaml
        <name1>-path.html
        <name2>-image.{jpg|png|...}
        ...
    <scope2>
        ...

The segmentation image must be a PNG the same size as the image, with the pixels corresponding to the lesion marked in red and the remaining pixels transparent.

The attributes file, if present, contains only one attribute, the diagnosis code as listed in search.js:

diagnosis: bcc

The path file, if present, contains the pathology report to be shown in DermShare.

dermshare's Issues

Missing result histogram if About tab showing when search completes

If a search completes while the About DermShare tab is selected, the result histogram does not appear.

OpenCV headers.

When trying to build dermshare, I had to change a few OpenCV include lines in autosegmenter/src/IPPInterface/IPPImage.h for everything to compile correctly. e.g. "cv.h" couldn't be found. Changing the import statements to <opencv/cv.h> fixed the problem. Submitting a pull request if upstream which upstream can use if they find it useful.

Server layout

Hi, My team and I have been working on the dermshare opendiamond implementation. We believe we have all dependency requirements met because each of the services appear to run (autosegementer, simplescope.py, blaster, dermshare.py, diamondd, dermshare_dataretriever.py, etc).

We split up the services across 4 servers in the following way:

• scopeserver - running simplescope.py
• dermclient - running dermshare.py
• jsonblaster - running /usr/local/bin/blaster (without reverse proxy)
• diamond0 - running diamondd, redis and dermshare_dataretriever.py (with populated data folders)

All these services are

• listening on 0.0.0.0 with "-l 0.0.0.0" arguments
• on port 8080 which is mapped to port 80 with iptables
• running under the same nonroot user

Is this topology recommended? Would it be preferred to group the jsonblaster with diamond0 or separate the dataretriever? Are there any junctions where using localhost instead of an IP address in a config file are more supported? We separated the servers to aid in debugging such as reading logs, distinguishing cookiecutter arguments and scopecookie placements. Thanks

What is the cookiecutter command for autosegment-cookie?

What would be the cookiecutter command for autosegment-cookie if you have have 4 servers:

• scopeserver - 192.168.1.20
• dermclient - 192.168.1.30
• jsonblaster - 192.168.1.40
• diamond0 - 192.168.1.50

On which host to run the cookiecutter command for autosegment-cookie?

And on which host do you place the autosegment-cookie in /etc/dermshare/ ?

Thanks

Is simplescope.py scope server sufficient

Section "Scope server" of README.md says "An example scope server is provided in simplescope."
Is simplescope/simplescope.py fully functional and do we still need to configure ~/.diamond/CERTS ~/.diamond/NEWSCOPE files? Thanks