Cross-Validation (#17)

* fix & refactor CrossVal
* update CI
* update manifest
* refactoring

.shippable.yml

@@ -52,40 +52,6 @@ script:
   - python setup.py check -m -s
   - flake8 . --ignore=E402,E731 --max-line-length=100
 
-  # ANNOTATION section
-  - 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 -a "data_images/drosophila_ovary_slice/annot_struct/*.png" -s "data_images/drosophila_ovary_slice/segm/*.png" --visual
-  - python experiments_segmentation/run_segm_slic_model_graphcut.py -i "data_images/drosophila_disc/image/img_[5,6].jpg" -cfg ./experiments_segmentation/sample_config.json --visual
-  - python experiments_segmentation/run_segm_slic_classif_graphcut.py -l data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv -i "data_images/drosophila_ovary_slice/image/insitu41*.jpg" -cfg ./experiments_segmentation/sample_config.json --visual
-
-  # CENTER DETECT. section
-  - rm -r -f results && mkdir results
-  - python experiments_ovary_centres/run_create_annotation.py
-  - python experiments_ovary_centres/run_center_candidate_training.py
-  - python experiments_ovary_centres/run_center_prediction.py
-  - python experiments_ovary_centres/run_center_clustering.py
-  - python experiments_ovary_centres/run_center_evaluation.py
-
-  # download MorphSnake
-  - pip install git+https://github.com/Borda/morph-snakes.git
-  # REGION GROWING section
-  - rm -r -f results && mkdir results
-  - python experiments_ovary_detect/run_RG2Sp_estim_shape-models.py
-  - python experiments_ovary_detect/run_ovary_egg-segmentation.py -m ellipse_moments ellipse_ransac_mmt ellipse_ransac_crit GC_pixels-large GC_pixels-shape GC_slic-small GC_slic-shape rg2sp_greedy-single rg2sp_GC-mixture watershed_morph
-  - python experiments_ovary_detect/run_ovary_segm_evaluation.py
-  - python experiments_ovary_detect/run_export_user-annot-segm.py
-  - python experiments_ovary_detect/run_cut_segmented_objects.py
-  - python experiments_ovary_detect/run_ellipse_annot_match.py
-  - python experiments_ovary_detect/run_ellipse_cut_scale.py
-  - python experiments_ovary_detect/run_egg_swap_orientation.py
-
 after_success:
   - python setup.py install
 

.travis.yml

@@ -48,9 +48,16 @@ script:
 
 after_success:
   - codecov  # public repository on Travis CI
-  # private repository on Travis CI
-  # - codecov -t 80efed4e-ac2b-4fea-a642-0a8b1c82e1c8
   - coverage xml
   - python-codacy-coverage -r coverage.xml
   - coverage report
+  # ANNOTATION section
+  - bash handling_annotations/test_annotations.sh
+  # SEGMENTATION section
+  - bash experiments_segmentation/test_segmentations.sh
+  # CENTER DETECT. section
+  - bash experiments_ovary_centres/test_ovary_cebters.sh
+  # REGION GROWING section
+  - bash experiments_ovary_detect/test_ovary_detect.sh
+  # test installed package
   - cd .. && python -c "import imsegm.descriptors"

MANIFEST.in

@@ -21,8 +21,8 @@ include setup.*
 # Exclude build configs
 exclude *.yml
 
-# Exclude tests
-exclude test*.py
+# Exclude experiments
+exclude */*.sh
 
 # Include the experiments
 recursive-include experiments_* *.py *.json

README.md

@@ -90,15 +90,19 @@ Moreover, we are using python [GraphCut wrapper](https://github.com/Borda/pyGCO)
 
 **Compilation**
 
-We have implemented cython version of some functions, especially computing descriptors, which require to compile them before using them
+We have implemented `cython` version of some functions, especially computing descriptors, which require to compile them before using them
 ```bash
 python setup.py build_ext --inplace
 ```
 If loading of compiled descriptors in `cython` fails, it is automatically swapped to `numpy` which gives the same results, but it is significantly slower.
 
 **Installation**
 
-The package can be installed via pip from the folder
+The package can be installed via pip 
+```bash
+pip install git+https://github.com/Borda/pyImSegm.git
+```
+ or using `setuptools` from local folder 
 ```bash
 python setup.py install
 ```

circle.yml

@@ -35,48 +35,16 @@ jobs:
               flake8 . --ignore=E402,E731 --max-line-length=100
 
         # ANNOTATION section
-        - run:
-            name: Annotations
-            command: |
-              python handling_annotations/run_image_color_quantization.py -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png"
-              python handling_annotations/run_image_color_quantization.py -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" -m position
-              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_image_convert_label_color.py -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" -out ./data_images/drosophila_ovary_slice/segm
-              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
+        - run: bash handling_annotations/test_annotations.sh
 
         # SEGMENTATION section
-        - run:
-            name: Segmentation
-            command: |
-              python experiments_segmentation/run_compute_stat_annot_segm.py -a "data_images/drosophila_ovary_slice/annot_struct/*.png" -s "data_images/drosophila_ovary_slice/segm/*.png" --visual
-              python experiments_segmentation/run_segm_slic_model_graphcut.py -i "data_images/drosophila_disc/image/img_[5,6].jpg" -cfg ./experiments_segmentation/sample_config.json --visual
-              python experiments_segmentation/run_segm_slic_classif_graphcut.py -l data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv -i "data_images/drosophila_ovary_slice/image/insitu41*.jpg" -cfg ./experiments_segmentation/sample_config.json --visual
+        - run: bash experiments_segmentation/test_segmentations.sh
 
         # CENTER DETECT. section
-        - run:
-            name: Center detection
-            command: |
-              python experiments_ovary_centres/run_create_annotation.py
-              python experiments_ovary_centres/run_center_candidate_training.py
-              python experiments_ovary_centres/run_center_prediction.py
-              python experiments_ovary_centres/run_center_clustering.py
-              python experiments_ovary_centres/run_center_evaluation.py
+        - run: bash experiments_ovary_centres/test_ovary_cebters.sh
 
         # REGION GROWING section
-        - run:
-            name: Region Growing
-            command: |
-              pip install --user git+https://github.com/Borda/morph-snakes.git
-              python experiments_ovary_detect/run_RG2Sp_estim_shape-models.py
-              python experiments_ovary_detect/run_ovary_egg-segmentation.py -m ellipse_moments ellipse_ransac_mmt ellipse_ransac_crit GC_pixels-large GC_pixels-shape GC_slic-small GC_slic-shape rg2sp_greedy-single rg2sp_GC-mixture watershed_morph
-              python experiments_ovary_detect/run_ovary_segm_evaluation.py --visual
-              python experiments_ovary_detect/run_export_user-annot-segm.py
-              python experiments_ovary_detect/run_cut_segmented_objects.py
-              python experiments_ovary_detect/run_ellipse_annot_match.py
-              python experiments_ovary_detect/run_ellipse_cut_scale.py
-              python experiments_ovary_detect/run_egg_swap_orientation.py
+        - run: bash experiments_ovary_detect/test_ovary_detect.sh
 
         # PASSING
         - run:

experiments_ovary_centres/run_center_clustering.py

@@ -66,7 +66,7 @@ def cluster_center_candidates(points, max_dist=100, min_samples=1):
     :return (ndarray, [int]):
     """
     points = np.array(points)
-    if len(points) == 0:
+    if not list(points):
         return points, []
     dbscan = cluster.DBSCAN(eps=max_dist, min_samples=min_samples)
     dbscan.fit(points)
@@ -134,7 +134,7 @@ def cluster_points_draw_export(dict_row, params, path_out=None):
         'missing some required fields: %s' % repr(dict_row)
     name = os.path.splitext(os.path.basename(dict_row['path_points']))[0]
     points = tl_data.load_landmarks_csv(dict_row['path_points'])
-    if len(points) == 0:
+    if not list(points):
         logging.debug('no points to cluster for "%s"', name)
     points = tl_data.swap_coord_x_y(points)
 

experiments_ovary_centres/test_ovary_cebters.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+rm -r -f results && mkdir results
+python experiments_ovary_centres/run_create_annotation.py
+python experiments_ovary_centres/run_center_candidate_training.py
+python experiments_ovary_centres/run_center_prediction.py
+python experiments_ovary_centres/run_center_clustering.py
+python experiments_ovary_centres/run_center_evaluation.py

experiments_ovary_detect/run_ovary_egg-segmentation.py

@@ -701,7 +701,7 @@ def image_segmentation(idx_row, params, debug_export=DEBUG_EXPORT):
         return name
     centers = tl_data.load_landmarks_csv(row_path['path_centers'])
     centers = tl_data.swap_coord_x_y(centers)
-    if len(centers) == 0:
+    if not list(centers):
         logging.warning('no center was detected for "%s"', name)
         return name
     # img = seg / float(seg.max())

experiments_ovary_detect/test_ovary_detect.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+pip install --user git+https://github.com/Borda/morph-snakes.git
+rm -r -f results && mkdir results
+python experiments_ovary_detect/run_RG2Sp_estim_shape-models.py
+python experiments_ovary_detect/run_ovary_egg-segmentation.py \
+    -m ellipse_moments ellipse_ransac_mmt ellipse_ransac_crit GC_pixels-large GC_pixels-shape GC_slic-small GC_slic-shape rg2sp_greedy-single rg2sp_GC-mixture watershed_morph
+python experiments_ovary_detect/run_ovary_segm_evaluation.py --visual
+python experiments_ovary_detect/run_export_user-annot-segm.py
+python experiments_ovary_detect/run_cut_segmented_objects.py
+python experiments_ovary_detect/run_ellipse_annot_match.py
+python experiments_ovary_detect/run_ellipse_cut_scale.py
+python experiments_ovary_detect/run_egg_swap_orientation.py

experiments_segmentation/run_segm_slic_model_graphcut.py

@@ -509,7 +509,7 @@ def main(params):
         tl_expt.create_subfolders(params['path_exp'], LIST_FOLDERS_DEBUG)
 
     paths_img = load_path_images(params)
-    assert len(paths_img) > 0, 'missing images'
+    assert paths_img, 'missing images'
 
     def _path_expt(n):
         return os.path.join(params['path_exp'], n)

experiments_segmentation/test_segmentations.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+rm -r -f results && mkdir results
+python experiments_segmentation/run_compute_stat_annot_segm.py \
+    -a "data_images/drosophila_ovary_slice/annot_struct/*.png" \
+    -s "data_images/drosophila_ovary_slice/segm/*.png" \
+    --visual
+python experiments_segmentation/run_segm_slic_model_graphcut.py \
+    -i "data_images/drosophila_disc/image/img_[5,6].jpg" \
+    -cfg ./experiments_segmentation/sample_config.json \
+    --visual
+python experiments_segmentation/run_segm_slic_classif_graphcut.py \
+    -l data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv \
+    -i "data_images/drosophila_ovary_slice/image/insitu41*.jpg" \
+    -cfg ./experiments_segmentation/sample_config.json \
+    --visual

handling_annotations/test_annotations.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+python handling_annotations/run_image_color_quantization.py \
+    -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png"
+python handling_annotations/run_image_color_quantization.py \
+    -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" \
+    -m position
+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_image_convert_label_color.py \
+    -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" \
+    -out ./data_images/drosophila_ovary_slice/segm
+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