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acil-bwh / ChestImagingPlatform

Chest Imaging Platform (CIP)
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feature request: please add install target to CMAKE #16

Open kayhan-batmanghelich opened 7 years ago

kayhan-batmanghelich commented 7 years ago

Hi,

This is a feature request not an issue. If possible, please add install target to the CMakeList. It is quite useful for the python extension. Currently, I am setting up my PYTHONPATH to the cip_python in the build folder and manually append teem-build/bin and CIP-build/bin tom my PATH.Not sure it is the best way. Also it seems ITKToolkit is also a requirement.

Thanks, Kayhan

rjosest commented 7 years ago

Hi Kayhan,

Thank you for your feedback. You bring a good point about the install target. We can definitely install all the binaries in a central place. Nevertheless, the PATH variable will have to be set to point to that install. Feel free to do a pull request if you make any modifications. We will happily review your changes and integrate them in the code.

Regarding ITKToolkit, some scripts were using it in early implementations but any operation could be replaced by a CIP CLI by now. What is the tool that you use that depends on ITKToolkit? We could update that as well.

Thanks for all your feedback and helping us debug the code.

Thanks

/R

On Feb 13, 2017, at 7:10 PM, Kayhan Batmanghelich notifications@github.com wrote:

Hi,

This is a feature request not an issue. If possible, please add install target to the CMakeList. It is quite useful for the python extension. Currently, I am setting up my PYTHONPATH to the cip_python in the build folder and manually append teem-build/bin and CIP-build/bin tom my PATH.Not sure it is the best way. Also it seems ITKToolkit is also a requirement.

Thanks, Kayhan

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kayhan-batmanghelich commented 7 years ago

Hi Raul,

My pleasure. It was this one:

./cip_python/utils/quick_airway_vessel_segmentation.py

some of the paths were hard coded.

Perhaps, I have to open a new issue or ask in the google group. I am looking for a pipeline to create vessel mask. I have seen vessel particle pipeline but not the vessel mask. Does that exist? I can also ask in a new issue if needed.

Thanks,

rjosest commented 7 years ago

Hi Kayhan,

Thank you for letting us know. That path setting is not necessary anymore assuming you have the tools in the proper location.

Nevertheless, the core tool in that python tool is the ComputeFeatureStrength CLI. That CLI can extract a vessel/airway masks based on the Frangi filter. You could directly use that output and select a given threshold to define the cut-off. That could be use as an initial mask. You can see in quick_airway_vessel_segmentation.py how ComputeFeatureStrenght is called.

/R

On Feb 13, 2017, at 7:48 PM, Kayhan Batmanghelich notifications@github.com wrote:

Hi Raul,

My pleasure. It was this one:

./cip_python/utils/quick_airway_vessel_segmentation.py some of the paths were hard coded.

Perhaps, I have to open a new issue or ask in the google group. I am looking for a pipeline to create vessel mask. I have seen vessel particle pipeline but not the vessel mask. Does that exist? I can also ask in a new issue if needed.

Thanks,

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/acil-bwh/ChestImagingPlatform/issues/16#issuecomment-279572050, or mute the thread https://github.com/notifications/unsubscribe-auth/ADD8krzz-N09mNsteet48DXRVTBN0Umkks5rcPnQgaJpZM4L_5MR.

kayhan-batmanghelich commented 7 years ago

Thanks Raul.