update segmentations (#6)

 * rename internal function
 * update manifest
 * rename local _wrapper
 * code cleaning
 * unify segm. models
 * move images -> data_images
 * add Langer. islets images
 * optionally missing params
 * add using segm. config
 * update annots
 * fix segm. debug show
 * check segm. features
 * regroup general images
 * update colors for visual @segm
 * update arg params @segm
 * add label boundary
 * fix classif. stat
 * add unsuper. model
 * update (c)
 * add mv Otsu threshold
 * update compute stat @segm
 * add color mGrad
 * update doc

Author: Borda

.shippable.yml

@@ -49,17 +49,17 @@ script:
   - nosetests -v --exe --with-doctest --with-xunit --with-coverage --cover-package=imsegm --xunit-file=$CI_REPORTS/nosetests.xml
 
   # ANNOTATION section
-  - python handling_annotations/run_image_color_quantization.py -imgs "images/drosophila_ovary_slice/segm_rgb/*.png"
-  - python handling_annotations/run_image_convert_label_color.py -imgs "images/drosophila_ovary_slice/segm/*.png" -out images/drosophila_ovary_slice/segm_rgb
-  - python handling_annotations/run_overlap_images_segms.py  -imgs "images/drosophila_ovary_slice/image/*.jpg" -segs images/drosophila_ovary_slice/segm -out results/overlap_ovary_segment
-  - python handling_annotations/run_segm_annot_inpaint.py -imgs "images/drosophila_ovary_slice/segm/*.png" --label 0
-  - python handling_annotations/run_segm_annot_relabel.py -imgs "images/drosophila_ovary_slice/center_levels/*.png" -out results/relabel_center_levels
+  - python handling_annotations/run_image_color_quantization.py -imgs "data_images/drosophila_ovary_slice/segm_rgb/*.png"
+  - python handling_annotations/run_image_convert_label_color.py -imgs "data_images/drosophila_ovary_slice/segm/*.png" -out data_images/drosophila_ovary_slice/segm_rgb
+  - python handling_annotations/run_overlap_images_segms.py  -imgs "data_images/drosophila_ovary_slice/image/*.jpg" -segs data_images/drosophila_ovary_slice/segm -out results/overlap_ovary_segment
+  - python handling_annotations/run_segm_annot_inpaint.py -imgs "data_images/drosophila_ovary_slice/segm/*.png" --label 0
+  - python handling_annotations/run_segm_annot_relabel.py -imgs "data_images/drosophila_ovary_slice/center_levels/*.png" -out results/relabel_center_levels
 
   # SEGMENTATION section
   - rm -r -f results && mkdir results
-  - python experiments_segmentation/run_compute-stat_annot-segm.py
-  - python experiments_segmentation/run_segm_slic_model_graphcut.py --nb_jobs 1
-  - python experiments_segmentation/run_segm_slic_classif_graphcut.py --nb_jobs 1
+  - python experiments_segmentation/run_compute_stat_annot_segm.py --visual
+  - python experiments_segmentation/run_segm_slic_model_graphcut.py --path_config experiments_segmentation/sample_config.json --nb_jobs 1
+  - python experiments_segmentation/run_segm_slic_classif_graphcut.py --path_config experiments_segmentation/sample_config.json --nb_jobs 1
 
   # CENTER DETECT. section
   - rm -r -f results && mkdir results

MANIFEST.in

@@ -1,2 +1,3 @@
 include README.md
+include LICENSE
 include requirements.txt

README.md

@@ -35,18 +35,18 @@ test:
     - coverage report && coverage xml -o $CIRCLE_TEST_REPORTS/coverage.xml
 
     # ANNOTATION section
-    - unset DISPLAY && python handling_annotations/run_image_color_quantization.py -imgs "images/drosophila_ovary_slice/segm_rgb/*.png"
-    - unset DISPLAY && python handling_annotations/run_image_color_quantization.py -imgs "images/drosophila_ovary_slice/segm_rgb/*.png" -m position
-    - unset DISPLAY && python handling_annotations/run_image_convert_label_color.py -imgs "images/drosophila_ovary_slice/segm/*.png" -out images/drosophila_ovary_slice/segm_rgb
-    - unset DISPLAY && python handling_annotations/run_image_convert_label_color.py -imgs "images/drosophila_ovary_slice/segm_rgb/*.png" -out images/drosophila_ovary_slice/segm
-    - unset DISPLAY && python handling_annotations/run_overlap_images_segms.py  -imgs "images/drosophila_ovary_slice/image/*.jpg" -segs images/drosophila_ovary_slice/segm -out results/overlap_ovary_segment
-    - unset DISPLAY && python handling_annotations/run_segm_annot_inpaint.py -imgs "images/drosophila_ovary_slice/segm/*.png" --label 0
-    - unset DISPLAY && python handling_annotations/run_segm_annot_relabel.py -imgs "images/drosophila_ovary_slice/center_levels/*.png" -out results/relabel_center_levels
+    - unset DISPLAY && python handling_annotations/run_image_color_quantization.py -imgs "data_images/drosophila_ovary_slice/segm_rgb/*.png"
+    - unset DISPLAY && python handling_annotations/run_image_color_quantization.py -imgs "data_images/drosophila_ovary_slice/segm_rgb/*.png" -m position
+    - unset DISPLAY && python handling_annotations/run_image_convert_label_color.py -imgs "data_images/drosophila_ovary_slice/segm/*.png" -out data_images/drosophila_ovary_slice/segm_rgb
+    - unset DISPLAY && python handling_annotations/run_image_convert_label_color.py -imgs "data_images/drosophila_ovary_slice/segm_rgb/*.png" -out data_images/drosophila_ovary_slice/segm
+    - unset DISPLAY && python handling_annotations/run_overlap_images_segms.py  -imgs "data_images/drosophila_ovary_slice/image/*.jpg" -segs data_images/drosophila_ovary_slice/segm -out results/overlap_ovary_segment
+    - unset DISPLAY && python handling_annotations/run_segm_annot_inpaint.py -imgs "data_images/drosophila_ovary_slice/segm/*.png" --label 0
+    - unset DISPLAY && python handling_annotations/run_segm_annot_relabel.py -imgs "data_images/drosophila_ovary_slice/center_levels/*.png" -out results/relabel_center_levels
 
     # SEGMENTATION section
-    - unset DISPLAY && python experiments_segmentation/run_compute-stat_annot-segm.py
-    - unset DISPLAY && python experiments_segmentation/run_segm_slic_model_graphcut.py --visual
-    - unset DISPLAY && python experiments_segmentation/run_segm_slic_classif_graphcut.py --visual
+    - unset DISPLAY && python experiments_segmentation/run_compute_stat_annot_segm.py --visual
+    - unset DISPLAY && python experiments_segmentation/run_segm_slic_model_graphcut.py --path_config experiments_segmentation/sample_config.json --visual
+    - unset DISPLAY && python experiments_segmentation/run_segm_slic_classif_graphcut.py --path_config experiments_segmentation/sample_config.json --visual
 
     # CENTER DETECT. section
     - unset DISPLAY && python experiments_ovary_centres/run_create_annotation.py

circle.yml

@@ -0,0 +1,11 @@
+,path_image,path_annot
+1,data_images/drosophila_disc/image/img_5.jpg,data_images/drosophila_disc/annot/img_5.png
+2,data_images/drosophila_disc/image/img_6.jpg,data_images/drosophila_disc/annot/img_6.png
+3,data_images/drosophila_disc/image/img_12.jpg,data_images/drosophila_disc/annot/img_12.png
+4,data_images/drosophila_disc/image/img_14.jpg,data_images/drosophila_disc/annot/img_14.png
+5,data_images/drosophila_disc/image/img_15.jpg,data_images/drosophila_disc/annot/img_15.png
+6,data_images/drosophila_disc/image/img_19.jpg,data_images/drosophila_disc/annot/img_19.png
+7,data_images/drosophila_disc/image/img_20.jpg,data_images/drosophila_disc/annot/img_20.png
+8,data_images/drosophila_disc/image/img_24.jpg,data_images/drosophila_disc/annot/img_24.png
+9,data_images/drosophila_disc/image/img_26.jpg,data_images/drosophila_disc/annot/img_26.png
+10,data_images/drosophila_disc/image/img_43.jpg,data_images/drosophila_disc/annot/img_43.png

images/drosophila_disc/annot/img_12.png renamed to data_images/drosophila_disc/annot/img_12.png

@@ -0,0 +1,3 @@
+,path_image,path_annot
+1,data_images/drosophila_disc/image/img_6.jpg,data_images/drosophila_disc/annot/img_6.png
+2,data_images/drosophila_disc/image/img_43.jpg,data_images/drosophila_disc/annot/img_43.png

images/drosophila_disc/annot/img_14.png renamed to data_images/drosophila_disc/annot/img_14.png

@@ -0,0 +1,11 @@
+,path_image,path_annot
+1,data_images/drosophila_ovary_slice/image/insitu4174.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu4174.png
+2,data_images/drosophila_ovary_slice/image/insitu4358.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu4358.png
+3,data_images/drosophila_ovary_slice/image/insitu7331.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu7331.png
+4,data_images/drosophila_ovary_slice/image/insitu7544.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu7544.png
+5,data_images/drosophila_ovary_slice/image/insitu7545.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu7545.png
+6,data_images/drosophila_ovary_slice/image/insitu4174.tif,data_images/drosophila_ovary_slice/annot_struct/insitu4174.png
+7,data_images/drosophila_ovary_slice/image/insitu4358.tif,data_images/drosophila_ovary_slice/annot_struct/insitu4358.png
+8,data_images/drosophila_ovary_slice/image/insitu7331.tif,data_images/drosophila_ovary_slice/annot_struct/insitu7331.png
+9,data_images/drosophila_ovary_slice/image/insitu7544.tif,data_images/drosophila_ovary_slice/annot_struct/insitu7544.png
+10,data_images/drosophila_ovary_slice/image/insitu7545.tif,data_images/drosophila_ovary_slice/annot_struct/insitu7545.png

images/drosophila_disc/annot/img_15.png renamed to data_images/drosophila_disc/annot/img_15.png

@@ -0,0 +1,3 @@
+,path_image,path_annot
+1,data_images/drosophila_ovary_slice/image/insitu4174.jpg,data_images/drosophila_ovary_slice/annot_struct/insitu4174.png
+2,data_images/drosophila_ovary_slice/image/insitu7545.tif,data_images/drosophila_ovary_slice/annot_struct/insitu7545.png

images/drosophila_disc/annot/img_19.png renamed to data_images/drosophila_disc/annot/img_19.png

@@ -0,0 +1,6 @@
+,path_image,path_centers,path_annot,path_segm
+1,data_images/drosophila_ovary_slice/image/insitu4174.tif,data_images/drosophila_ovary_slice/center_levels/insitu4174.png,data_images/drosophila_ovary_slice/annot_eggs/insitu4174.png,data_images/drosophila_ovary_slice/segm/insitu4174.png
+2,data_images/drosophila_ovary_slice/image/insitu4358.tif,data_images/drosophila_ovary_slice/center_levels/insitu4358.png,data_images/drosophila_ovary_slice/annot_eggs/insitu4358.png,data_images/drosophila_ovary_slice/segm/insitu4358.png
+3,data_images/drosophila_ovary_slice/image/insitu7331.tif,data_images/drosophila_ovary_slice/center_levels/insitu7331.png,data_images/drosophila_ovary_slice/annot_eggs/insitu7331.png,data_images/drosophila_ovary_slice/segm/insitu7331.png
+4,data_images/drosophila_ovary_slice/image/insitu7544.tif,data_images/drosophila_ovary_slice/center_levels/insitu7544.png,data_images/drosophila_ovary_slice/annot_eggs/insitu7544.png,data_images/drosophila_ovary_slice/segm/insitu7544.png
+5,data_images/drosophila_ovary_slice/image/insitu7545.tif,data_images/drosophila_ovary_slice/center_levels/insitu7545.png,data_images/drosophila_ovary_slice/annot_eggs/insitu7545.png,data_images/drosophila_ovary_slice/segm/insitu7545.png

images/drosophila_disc/annot/img_20.png renamed to data_images/drosophila_disc/annot/img_20.png

@@ -0,0 +1,3 @@
+,path_image,path_centers,path_annot,path_segm
+1,data_images/drosophila_ovary_slice/image/insitu4358.jpg,data_images/drosophila_ovary_slice/center_levels/insitu4358.png,data_images/drosophila_ovary_slice/annot_eggs/insitu4358.png,data_images/drosophila_ovary_slice/segm/insitu4358.png
+2,data_images/drosophila_ovary_slice/image/insitu7545.tif,data_images/drosophila_ovary_slice/center_levels/insitu7545.png,data_images/drosophila_ovary_slice/annot_eggs/insitu7545.png,data_images/drosophila_ovary_slice/segm/insitu7545.png

images/drosophila_disc/annot/img_24.png renamed to data_images/drosophila_disc/annot/img_24.png

@@ -0,0 +1,6 @@
+,path_image,path_centers,path_annot,path_segm
+1,data_images/drosophila_ovary_slice/image/insitu4174.jpg,data_images/drosophila_ovary_slice/center_levels/insitu4174.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu4174.png,data_images/drosophila_ovary_slice/segm/insitu4174.png
+2,data_images/drosophila_ovary_slice/image/insitu4358.jpg,data_images/drosophila_ovary_slice/center_levels/insitu4358.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu4358.png,data_images/drosophila_ovary_slice/segm/insitu4358.png
+3,data_images/drosophila_ovary_slice/image/insitu7331.jpg,data_images/drosophila_ovary_slice/center_levels/insitu7331.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu7331.png,data_images/drosophila_ovary_slice/segm/insitu7331.png
+4,data_images/drosophila_ovary_slice/image/insitu7544.jpg,data_images/drosophila_ovary_slice/center_levels/insitu7544.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu7544.png,data_images/drosophila_ovary_slice/segm/insitu7544.png
+5,data_images/drosophila_ovary_slice/image/insitu7545.jpg,data_images/drosophila_ovary_slice/center_levels/insitu7545.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu7545.png,data_images/drosophila_ovary_slice/segm/insitu7545.png

images/drosophila_disc/annot/img_26.png renamed to data_images/drosophila_disc/annot/img_26.png

@@ -0,0 +1,3 @@
+,path_image,path_centers,path_annot,path_segm
+1,data_images/drosophila_ovary_slice/image/insitu4358.jpg,data_images/drosophila_ovary_slice/center_levels/insitu4358.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu4358.png,data_images/drosophila_ovary_slice/segm/insitu4358.png
+2,data_images/drosophila_ovary_slice/image/insitu7545.tif,data_images/drosophila_ovary_slice/center_levels/insitu7545.csv,data_images/drosophila_ovary_slice/annot_eggs/insitu7545.png,data_images/drosophila_ovary_slice/segm/insitu7545.png