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Injectionsite #20

Merged
merged 2 commits into from
Apr 15, 2020
Merged

Injectionsite #20

merged 2 commits into from
Apr 15, 2020

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stephenlenzi
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  • removes some hard code
  • removes a couple of redundant functions.
  • removes cellfinder and amap dependencies, moving these to imlib or neuro.
  • moves paths from amap to neuro
  • moves amap_vis to neuro
  • makes visualise directory for visualisation backends (i.e. amap vis and others tbd)

@adamltyson adamltyson self-assigned this Apr 15, 2020
@adamltyson adamltyson merged commit 5417e3d into SainsburyWellcomeCentre:injectionsite Apr 15, 2020
adamltyson added a commit that referenced this pull request Apr 16, 2020
@adamltyson @FedeClaudi @stephenlenzi
Refactor imports (#21)
ae09539 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 17, 2020
@adamltyson @FedeClaudi @stephenlenzi
Add manual segmentation (#23)
5b98fc1 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 20, 2020
@adamltyson @FedeClaudi @stephenlenzi
Support multiple regions (#26)
2e02dd2 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

* update docs

* update docs

* update docs

* update docs

* support multiple objects

* color objects

* bump

* update reqs

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 22, 2020
@adamltyson @FedeClaudi @stephenlenzi
bump (#27)
33573d5 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

* update docs

* update docs

* update docs

* update docs

* support multiple objects

* color objects

* bump

* update reqs

* improve rendering of flat objects

* bump

* prevent saving unnecessary common volume

* allow ROIs to be edited

* label regions

* bump

* bump

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
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@stephenlenzi @adamltyson