From 9a985157ff86edbb55efa6b364a304c47a456d9a Mon Sep 17 00:00:00 2001 From: "J. Borovec" Date: Tue, 14 Apr 2020 20:45:56 +0200 Subject: [PATCH] minor refactoring * rename data-images * add pep8speaks * move figures * docs preview * update config --- .pep8speaks.yml | 28 +++++++ MANIFEST.in | 26 +++--- README.md | 78 +++++++++--------- .../_figures => assets}/imag-disk-20_gmm.jpg | Bin .../imag-disk-20_train.jpg | Bin .../insitu7544_ellipses.jpg | Bin .../source/_figures => assets}/insitu7545.jpg | Bin .../insitu7545_RG2SP-gc-mm.png | Bin .../insitu7545_RG2SP_animation.gif | Bin .../insitu7545_center_clusters.jpg | Bin .../insitu7545_ellipse_fit.png | Bin .../_figures => assets}/insitu7545_gc.png | Bin .../insitu7545_user-annot-segm.jpg | Bin .../schema_slic-fts-clf-gc.jpg | Bin .../segm-visual_D03_sy04_100x.jpg | Bin .../visual_img_43_debug.jpg | Bin circle.yml | 5 ++ .../drosophila_disc/annot/img_12.png | Bin .../drosophila_disc/annot/img_14.png | Bin .../drosophila_disc/annot/img_15.png | Bin .../drosophila_disc/annot/img_19.png | Bin 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.../synthetic/texture-2_gray.jpg | Bin .../synthetic/texture-3-small_annot.png | Bin .../synthetic/texture-3-small_gray.jpg | Bin .../synthetic/texture_rgb_3cls.jpg | Bin .../drosophila_disc/list_imaginal-disks.csv | 11 --- .../list_imaginal-disks_short.csv | 3 - .../list_imgs-annot-struct.csv | 11 --- .../list_imgs-segm-center-levels.csv | 6 -- .../list_imgs-segm-center-levels_short.csv | 3 - .../list_imgs-segm-center-points.csv | 6 -- .../list_imgs-segm-center-points_short.csv | 3 - .../list_lang-isl_imgs-annot-2.csv | 5 -- .../list_lang-isl_imgs-annot.csv | 4 - docs/source/conf.py | 11 +-- .../gui_annot_center_correction.py | 2 +- .../run_center_candidate_training.py | 8 +- .../run_center_evaluation.py | 4 +- .../run_center_prediction.py | 4 +- .../run_RG2Sp_estim_shape-models.py | 4 +- .../run_cut_segmented_objects.py | 6 +- .../run_egg_swap_orientation.py | 2 +- .../run_ellipse_annot_match.py | 2 +- .../run_ellipse_cut_scale.py | 2 +- .../run_export_user-annot-segm.py | 2 +- .../run_ovary_egg-segmentation.py | 4 +- .../run_ovary_segm_evaluation.py | 2 +- .../run_compute_stat_annot_segm.py | 6 +- .../run_eval_superpixels.py | 6 +- .../run_segm_slic_classif_graphcut.py | 6 +- .../run_segm_slic_model_graphcut.py | 8 +- .../test_segmentations.sh | 10 +-- .../run_image_color_quantization.py | 4 +- .../run_image_convert_label_color.py | 10 +-- .../run_overlap_images_segms.py | 4 +- .../run_segm_annot_inpaint.py | 4 +- .../run_segm_annot_relabel.py | 4 +- handling_annotations/test_annotations.sh | 20 ++--- imsegm/__init__.py | 2 +- imsegm/annotation.py | 2 +- imsegm/utilities/data_io.py | 18 ++-- imsegm/utilities/data_samples.py | 2 +- imsegm/utilities/read_zvi.py | 2 +- notebooks/RG2Sp_model_region-grow.ipynb | 4 +- notebooks/RG2Sp_region-growing.ipynb | 4 +- notebooks/RG2Sp_shape-models.ipynb | 4 +- .../egg-center_candidates-clustering.ipynb | 2 +- notebooks/egg-detect_ellipse-fitting.ipynb | 2 +- notebooks/egg_segment_graphcut.ipynb | 2 +- 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100644 data_images/langerhans_islets/list_lang-isl_imgs-annot-2.csv delete mode 100644 data_images/langerhans_islets/list_lang-isl_imgs-annot.csv delete mode 100644 pytest.ini diff --git a/.pep8speaks.yml b/.pep8speaks.yml new file mode 100644 index 00000000..1a35e809 --- /dev/null +++ b/.pep8speaks.yml @@ -0,0 +1,28 @@ +# File : .pep8speaks.yml + +scanner: + diff_only: True # If False, the entire file touched by the Pull Request is scanned for errors. If True, only the diff is scanned. + linter: pycodestyle # Other option is flake8 + +pycodestyle: # Same as scanner.linter value. Other option is flake8 + max-line-length: 110 # Default is 79 in PEP 8 + ignore: # Errors and warnings to ignore + - W504 # line break after binary operator + - E402 # module level import not at top of file + - E731 # do not assign a lambda expression, use a def + - C406 # Unnecessary list literal - rewrite as a dict literal. + - E741 # ambiguous variable name + +no_blank_comment: True # If True, no comment is made on PR without any errors. +descending_issues_order: False # If True, PEP 8 issues in message will be displayed in descending order of line numbers in the file + +message: # Customize the comment made by the bot, + opened: # Messages when a new PR is submitted + header: "Hello @{name}! Thanks for opening this PR. " + # The keyword {name} is converted into the author's username + footer: "Do see the [Hitchhiker's guide to code style](https://goo.gl/hqbW4r)" + # The messages can be written as they would over GitHub + updated: # Messages when new commits are added to the PR + header: "Hello @{name}! Thanks for updating this PR. " + footer: "" # Why to comment the link to the style guide everytime? :) + no_errors: "There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers: " diff --git a/MANIFEST.in b/MANIFEST.in index b8889c26..3adb72bd 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -34,20 +34,20 @@ recursive-include experiments_* *.py *.yml recursive-include handling_annotations *.py # Include the figures -recursive-include docs/source/_figures *.gif *.jpg *.png +recursive-include assets *.gif *.jpg *.png # Include the sample images -include data_images/others/lena.png - data_images/synthetic/reference.jpg - data_images/synthetic/texture_rgb_3cls.jpg - data_images/others/sea_starfish-2.jpg - data_images/histology_CIMA/29-041-Izd2-w35-CD31-3-les1.jpg - data_images/histology_Flagship/Case001_Cytokeratin.jpg - data_images/drosophila_disc/image/img_6.jpg - data_images/drosophila_disc/annot/img_6.png - data_images/drosophila_ovary_slice/image/insitu7545.jpg - data_images/drosophila_ovary_slice/annot_struct/insitu7545.png - data_images/langerhans_islets/image/gtExoIsl_21.jpg +include data-images/others/lena.png + data-images/synthetic/reference.jpg + data-images/synthetic/texture_rgb_3cls.jpg + data-images/others/sea_starfish-2.jpg + data-images/histology_CIMA/29-041-Izd2-w35-CD31-3-les1.jpg + data-images/histology_Flagship/Case001_Cytokeratin.jpg + data-images/drosophila_disc/image/img_6.jpg + data-images/drosophila_disc/annot/img_6.png + data-images/drosophila_ovary_slice/image/insitu7545.jpg + data-images/drosophila_ovary_slice/annot_struct/insitu7545.png + data-images/langerhans_islets/image/gtExoIsl_21.jpg prune .git prune .github @@ -55,7 +55,7 @@ prune libs prune venv prune build prune docs -prune data_images +prune data-images prune tests prune notebooks prune ij_macros diff --git a/README.md b/README.md index 0d3d5372..8f20fa0d 100755 --- a/README.md +++ b/README.md @@ -17,11 +17,11 @@ ## Superpixel segmentation with GraphCut regularisation -Image segmentation is widely used as an initial phase of many image processing tasks in computer vision and image analysis. Many recent segmentation methods use superpixels because they reduce the size of the segmentation problem by order of magnitude. Also, features on superpixels are much more robust than features on pixels only. We use spatial regularisation on superpixels to make segmented regions more compact. The segmentation pipeline comprises (i) computation of superpixels; (ii) extraction of descriptors such as colour and texture; (iii) soft classification, using a standard classifier for supervised learning, or the Gaussian Mixture Model for unsupervised learning; (iv) final segmentation using Graph Cut. We use this segmentation pipeline on real-world applications in medical imaging (see [sample images](data_images/). +Image segmentation is widely used as an initial phase of many image processing tasks in computer vision and image analysis. Many recent segmentation methods use superpixels because they reduce the size of the segmentation problem by order of magnitude. Also, features on superpixels are much more robust than features on pixels only. We use spatial regularisation on superpixels to make segmented regions more compact. The segmentation pipeline comprises (i) computation of superpixels; (ii) extraction of descriptors such as colour and texture; (iii) soft classification, using a standard classifier for supervised learning, or the Gaussian Mixture Model for unsupervised learning; (iv) final segmentation using Graph Cut. We use this segmentation pipeline on real-world applications in medical imaging (see [sample images](data-images/). We also show that [unsupervised segmentation](notebooks/segment-2d_slic-fts-clust-gc.ipynb) is sufficient for some situations, and provides similar results to those obtained using [trained segmentation](notebooks/segment-2d_slic-fts-classif-gc.ipynb). -![schema](docs/source/_figures/schema_slic-fts-clf-gc.jpg) +![schema](assets/schema_slic-fts-clf-gc.jpg) **Sample ipython notebooks:** * [Supervised segmentation](notebooks/segment-2d_slic-fts-classif-gc.ipynb) requires training annotation @@ -30,8 +30,8 @@ Image segmentation is widely used as an initial phase of many image processing t **Illustration** -![input image](docs/source/_figures/insitu7545.jpg) -![segmentation](docs/source/_figures/insitu7545_gc.png) +![input image](assets/insitu7545.jpg) +![segmentation](assets/insitu7545_gc.png) Reference: _Borovec J., Svihlik J., Kybic J., Habart D. (2017). **Supervised and unsupervised segmentation using superpixels, model estimation, and Graph Cut.** In: Journal of Electronic Imaging._ @@ -47,8 +47,8 @@ An image processing pipeline to detect and localize Drosophila egg chambers that **Illustration** -![estimated centres](docs/source/_figures/insitu7545_center_clusters.jpg) -![ellipse fitting](docs/source/_figures/insitu7545_ellipse_fit.png) +![estimated centres](assets/insitu7545_center_clusters.jpg) +![ellipse fitting](assets/insitu7545_ellipse_fit.png) Reference: _Borovec J., Kybic J., Nava R. (2017) **Detection and Localization of Drosophila Egg Chambers in Microscopy Images.** In: Machine Learning in Medical Imaging._ @@ -63,8 +63,8 @@ Region growing is a classical image segmentation method based on hierarchical re **Illustration** -![growing RG](docs/source/_figures/insitu7545_RG2SP_animation.gif) -![ellipse fitting](docs/source/_figures/insitu7545_RG2SP-gc-mm.png) +![growing RG](assets/insitu7545_RG2SP_animation.gif) +![ellipse fitting](assets/insitu7545_RG2SP-gc-mm.png) Reference: _Borovec J., Kybic J., Sugimoto, A. (2017). **Region growing using superpixels with learned shape prior.** In: Journal of Electronic Imaging._ @@ -134,26 +134,26 @@ We introduce some useful tools for work with image annotation and segmentation. * **Quantization:** in case you have some smooth colour labelling in your images you can remove them with following quantisation script. ```bash python handling_annotations/run_image_color_quantization.py \ - -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/segm_rgb/*.png" \ -m position -thr 0.01 --nb_workers 2 ``` * **Paint labels:** concerting image labels into colour space and other way around. ```bash 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 + -imgs "./data-images/drosophila_ovary_slice/segm/*.png" \ + -out ./data-images/drosophila_ovary_slice/segm_rgb ``` * **Visualisation:** having input image and its segmentation we can use simple visualisation which overlap the segmentation over input image. ```bash python handling_annotations/run_overlap_images_segms.py \ - -imgs "./data_images/drosophila_ovary_slice/image/*.jpg" \ - -segs ./data_images/drosophila_ovary_slice/segm \ + -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \ + -segs ./data-images/drosophila_ovary_slice/segm \ -out ./results/overlap_ovary_segment ``` * **In-painting** selected labels in segmentation. ```bash python handling_annotations/run_segm_annot_inpaint.py \ - -imgs "./data_images/drosophila_ovary_slice/segm/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/segm/*.png" \ --label 4 ``` * **Replace labels:** change labels in input segmentation into another set of labels in 1:1 schema. @@ -167,50 +167,50 @@ We introduce some useful tools for work with image annotation and segmentation. ### Semantic (un/semi)supervised segmentation We utilise (un)supervised segmentation according to given training examples or some expectations. -![vusial debug](docs/source/_figures/visual_img_43_debug.jpg) +![vusial debug](assets/visual_img_43_debug.jpg) * Evaluate superpixels (with given SLIC parameters) quality against given segmentation. It helps to find out the best SLIC configuration. ```bash python experiments_segmentation/run_eval_superpixels.py \ - -imgs "./data_images/drosophila_ovary_slice/image/*.jpg" \ - -segm "./data_images/drosophila_ovary_slice/annot_eggs/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \ + -segm "./data-images/drosophila_ovary_slice/annot_eggs/*.png" \ --img_type 2d_split \ --slic_size 20 --slic_regul 0.25 --slico ``` * Perform **Un-Supervised** segmentation in images given in CSV ```bash python experiments_segmentation/run_segm_slic_model_graphcut.py \ - -l ./data_images/langerhans_islets/list_lang-isl_imgs-annot.csv -i "" \ + -l ./data-images/langerhans_islets/list_lang-isl_imgs-annot.csv -i "" \ -cfg experiments_segmentation/sample_config.yml \ -o ./results -n langIsl --nb_classes 3 --visual --nb_workers 2 ``` OR specified on particular path: ```bash python experiments_segmentation/run_segm_slic_model_graphcut.py \ - -l "" -i "./data_images/langerhans_islets/image/*.jpg" \ + -l "" -i "./data-images/langerhans_islets/image/*.jpg" \ -cfg ./experiments_segmentation/sample_config.yml \ -o ./results -n langIsl --nb_classes 3 --visual --nb_workers 2 ``` - ![unsupervised](docs/source/_figures/imag-disk-20_gmm.jpg) + ![unsupervised](assets/imag-disk-20_gmm.jpg) * Perform **Supervised** segmentation with afterwards evaluation. ```bash python experiments_segmentation/run_segm_slic_classif_graphcut.py \ - -l ./data_images/drosophila_ovary_slice/list_imgs-annot-struct.csv \ - -i "./data_images/drosophila_ovary_slice/image/*.jpg" \ + -l ./data-images/drosophila_ovary_slice/list_imgs-annot-struct.csv \ + -i "./data-images/drosophila_ovary_slice/image/*.jpg" \ --path_config ./experiments_segmentation/sample_config.yml \ -o ./results -n Ovary --img_type 2d_split --visual --nb_workers 2 ``` - ![supervised](docs/source/_figures/imag-disk-20_train.jpg) + ![supervised](assets/imag-disk-20_train.jpg) * Perform **Semi-Supervised** is using the the supervised pipeline with not fully annotated images. * For both experiment you can evaluate segmentation results. ```bash python experiments_segmentation/run_compute-stat_annot-segm.py \ - -a "./data_images/drosophila_ovary_slice/annot_struct/*.png" \ + -a "./data-images/drosophila_ovary_slice/annot_struct/*.png" \ -s "./results/experiment_segm-supervise_ovary/*.png" \ - -i "./data_images/drosophila_ovary_slice/image/*.jpg" \ + -i "./data-images/drosophila_ovary_slice/image/*.jpg" \ -o ./results/evaluation --visual ``` - ![vusial](docs/source/_figures/segm-visual_D03_sy04_100x.jpg) + ![vusial](assets/segm-visual_D03_sy04_100x.jpg) The previous two (un)segmentation accept [configuration file](experiments_segmentation/sample_config.yml) (YAML) by parameter `-cfg` with some extra parameters which was not passed in arguments, for instance: ```yaml @@ -240,16 +240,16 @@ In general, the input is a formatted list (CSV file) of input images and annotat 1. With zone annotation, we train a classifier for centre candidate prediction. The annotation can be a CSV file with annotated centres as points, and the zone of positive examples is set uniformly as the circular neighbourhood around these points. Another way (preferable) is to use an annotated image with marked zones for positive, negative and neutral examples. ```bash python experiments_ovary_centres/run_center_candidate_training.py -list none \ - -segs "./data_images/drosophila_ovary_slice/segm/*.png" \ - -imgs "./data_images/drosophila_ovary_slice/image/*.jpg" \ - -centers "./data_images/drosophila_ovary_slice/center_levels/*.png" \ + -segs "./data-images/drosophila_ovary_slice/segm/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \ + -centers "./data-images/drosophila_ovary_slice/center_levels/*.png" \ -out ./results -n ovary ``` 1. Having trained classifier we perform center prediction composed from two steps: i) center candidate clustering and ii) candidate clustering. ```bash python experiments_ovary_centres/run_center_prediction.py -list none \ - -segs "./data_images/drosophila_ovary_slice/segm/*.png" \ - -imgs "./data_images/drosophila_ovary_slice/image/*.jpg" \ + -segs "./data-images/drosophila_ovary_slice/segm/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \ -centers ./results/detect-centers-train_ovary/classifier_RandForest.pkl \ -out ./results -n ovary ``` @@ -260,8 +260,8 @@ In general, the input is a formatted list (CSV file) of input images and annotat 1. This is just cut out clustering in case you want to use different parameters. ```bash python experiments_ovary_centres/run_center_clustering.py \ - -segs "./data_images/drosophila_ovary_slice/segm/*.png" \ - -imgs "./data_images/drosophila_ovary_slice/image/*.jpg" \ + -segs "./data-images/drosophila_ovary_slice/segm/*.png" \ + -imgs "./data-images/drosophila_ovary_slice/image/*.jpg" \ -centers "./results/detect-centers-train_ovary/candidates/*.csv" \ -out ./results ``` @@ -286,7 +286,7 @@ In general, the input is a formatted list (CSV file) of input images and annotat -out ~/Medical-drosophila/RESULTS/atlas_datasets/ovary_images/stage_3 ``` -![ellipse fitting](docs/source/_figures/insitu7544_ellipses.jpg) +![ellipse fitting](assets/insitu7544_ellipses.jpg) ### Region growing with a shape prior @@ -303,12 +303,12 @@ pip install --user git+https://github.com/Borda/morph-snakes.git ```bash python experiments_ovary_detect/run_RG2Sp_estim_shape-models.py \ -annot "~/Medical-drosophila/egg_segmentation/mask_2d_slice_complete_ind_egg/*.png" \ - -out ./data_images -nb 15 + -out ./data-images -nb 15 ``` 1. Run several segmentation techniques on each image. ```bash python experiments_ovary_detect/run_ovary_egg-segmentation.py \ - -list ./data_images/drosophila_ovary_slice/list_imgs-segm-center-points.csv \ + -list ./data-images/drosophila_ovary_slice/list_imgs-segm-center-points.csv \ -out ./results -n ovary_image --nb_workers 1 \ -m ellipse_moments \ ellipse_ransac_mmt \ @@ -328,15 +328,15 @@ pip install --user git+https://github.com/Borda/morph-snakes.git 1. In the end, cut individual segmented objects comes as minimal bounding box. ```bash python experiments_ovary_detect/run_cut_segmented_objects.py \ - -annot "./data_images/drosophila_ovary_slice/annot_eggs/*.png" \ - -img "./data_images/drosophila_ovary_slice/segm/*.png" \ + -annot "./data-images/drosophila_ovary_slice/annot_eggs/*.png" \ + -img "./data-images/drosophila_ovary_slice/segm/*.png" \ -out ./results/cut_images --padding 50 ``` 1. Finally, performing visualisation of segmentation results together with expert annotation. ```bash python experiments_ovary_detect/run_export_user-annot-segm.py ``` - ![user-annnot](docs/source/_figures/insitu7545_user-annot-segm.jpg) + ![user-annnot](assets/insitu7545_user-annot-segm.jpg) --- diff --git a/docs/source/_figures/imag-disk-20_gmm.jpg b/assets/imag-disk-20_gmm.jpg similarity index 100% rename from docs/source/_figures/imag-disk-20_gmm.jpg rename to assets/imag-disk-20_gmm.jpg diff --git a/docs/source/_figures/imag-disk-20_train.jpg b/assets/imag-disk-20_train.jpg similarity index 100% rename from docs/source/_figures/imag-disk-20_train.jpg rename to assets/imag-disk-20_train.jpg diff --git a/docs/source/_figures/insitu7544_ellipses.jpg b/assets/insitu7544_ellipses.jpg similarity index 100% rename from docs/source/_figures/insitu7544_ellipses.jpg rename to assets/insitu7544_ellipses.jpg diff --git a/docs/source/_figures/insitu7545.jpg b/assets/insitu7545.jpg similarity 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b/assets/visual_img_43_debug.jpg similarity index 100% rename from docs/source/_figures/visual_img_43_debug.jpg rename to assets/visual_img_43_debug.jpg diff --git a/circle.yml b/circle.yml index c6e33fdf..6b0322f6 100755 --- a/circle.yml +++ b/circle.yml @@ -122,6 +122,11 @@ jobs: - *install_pips # DOCUMENTATION - *make_docs + # PREVIEW + - store_artifacts: + # allows us to preview the generated html pages + path: docs/build/html/ + destination: html workflows: version: 2 diff --git a/data_images/drosophila_disc/annot/img_12.png b/data-images/drosophila_disc/annot/img_12.png old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_disc/annot/img_12.png rename to data-images/drosophila_disc/annot/img_12.png diff --git a/data_images/drosophila_disc/annot/img_14.png b/data-images/drosophila_disc/annot/img_14.png old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_disc/annot/img_14.png rename to 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data-images/drosophila_disc/image/img_26.jpg diff --git a/data_images/drosophila_disc/image/img_43.jpg b/data-images/drosophila_disc/image/img_43.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_disc/image/img_43.jpg rename to data-images/drosophila_disc/image/img_43.jpg diff --git a/data_images/drosophila_disc/image/img_5.jpg b/data-images/drosophila_disc/image/img_5.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_disc/image/img_5.jpg rename to data-images/drosophila_disc/image/img_5.jpg diff --git a/data_images/drosophila_disc/image/img_6.jpg b/data-images/drosophila_disc/image/img_6.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_disc/image/img_6.jpg rename to data-images/drosophila_disc/image/img_6.jpg diff --git a/data-images/drosophila_disc/list_imaginal-disks.csv b/data-images/drosophila_disc/list_imaginal-disks.csv new file mode 100644 index 00000000..f564ccce --- /dev/null +++ b/data-images/drosophila_disc/list_imaginal-disks.csv @@ -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 diff --git a/data-images/drosophila_disc/list_imaginal-disks_short.csv b/data-images/drosophila_disc/list_imaginal-disks_short.csv new file mode 100644 index 00000000..28eca76b --- /dev/null +++ b/data-images/drosophila_disc/list_imaginal-disks_short.csv @@ -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 diff --git a/data_images/drosophila_ovary_3D/AU10-13_f0011.tif b/data-images/drosophila_ovary_3D/AU10-13_f0011.tif old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_ovary_3D/AU10-13_f0011.tif rename to data-images/drosophila_ovary_3D/AU10-13_f0011.tif diff --git a/data_images/drosophila_ovary_slice/annot_eggs/insitu4174.png b/data-images/drosophila_ovary_slice/annot_eggs/insitu4174.png 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b/data-images/drosophila_ovary_slice/image_cut-stage-2/insitu7544.png similarity index 100% rename from data_images/drosophila_ovary_slice/image_cut-stage-2/insitu7544.png rename to data-images/drosophila_ovary_slice/image_cut-stage-2/insitu7544.png diff --git a/data_images/drosophila_ovary_slice/image_cut-stage-2/insitu7545.png b/data-images/drosophila_ovary_slice/image_cut-stage-2/insitu7545.png similarity index 100% rename from data_images/drosophila_ovary_slice/image_cut-stage-2/insitu7545.png rename to data-images/drosophila_ovary_slice/image_cut-stage-2/insitu7545.png diff --git a/data_images/drosophila_ovary_slice/info_ovary_images.txt b/data-images/drosophila_ovary_slice/info_ovary_images.txt old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_ovary_slice/info_ovary_images.txt rename to data-images/drosophila_ovary_slice/info_ovary_images.txt diff --git a/data_images/drosophila_ovary_slice/info_ovary_images_ellipses.csv b/data-images/drosophila_ovary_slice/info_ovary_images_ellipses.csv similarity index 100% rename from data_images/drosophila_ovary_slice/info_ovary_images_ellipses.csv rename to data-images/drosophila_ovary_slice/info_ovary_images_ellipses.csv diff --git a/data-images/drosophila_ovary_slice/list_imgs-annot-struct.csv b/data-images/drosophila_ovary_slice/list_imgs-annot-struct.csv new file mode 100644 index 00000000..056c8602 --- /dev/null +++ b/data-images/drosophila_ovary_slice/list_imgs-annot-struct.csv @@ -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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv b/data-images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv similarity index 51% rename from data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv rename to data-images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv index 67427076..fb0f0b44 100644 --- a/data_images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv +++ b/data-images/drosophila_ovary_slice/list_imgs-annot-struct_short.csv @@ -1,3 +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 +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 diff --git a/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv b/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv new file mode 100644 index 00000000..a2de1bcd --- /dev/null +++ b/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv @@ -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 diff --git a/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv b/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv new file mode 100644 index 00000000..889ad5cd --- /dev/null +++ b/data-images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv @@ -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 diff --git a/data-images/drosophila_ovary_slice/list_imgs-segm-center-points.csv b/data-images/drosophila_ovary_slice/list_imgs-segm-center-points.csv new file mode 100644 index 00000000..66809977 --- /dev/null +++ b/data-images/drosophila_ovary_slice/list_imgs-segm-center-points.csv @@ -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 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100755 new mode 100644 similarity index 100% rename from data_images/drosophila_ovary_slice/segm/insitu7331.png rename to data-images/drosophila_ovary_slice/segm/insitu7331.png diff --git a/data_images/drosophila_ovary_slice/segm/insitu7544.png b/data-images/drosophila_ovary_slice/segm/insitu7544.png old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_ovary_slice/segm/insitu7544.png rename to data-images/drosophila_ovary_slice/segm/insitu7544.png diff --git a/data_images/drosophila_ovary_slice/segm/insitu7545.png b/data-images/drosophila_ovary_slice/segm/insitu7545.png old mode 100755 new mode 100644 similarity index 100% rename from data_images/drosophila_ovary_slice/segm/insitu7545.png rename to data-images/drosophila_ovary_slice/segm/insitu7545.png diff --git a/data_images/drosophila_ovary_slice/segm_rgb/insitu4174.png b/data-images/drosophila_ovary_slice/segm_rgb/insitu4174.png old mode 100755 new mode 100644 similarity index 100% rename from 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b/data-images/langerhans_islets/image/Lh09-07.jpg similarity index 100% rename from data_images/langerhans_islets/image/Lh09-07.jpg rename to data-images/langerhans_islets/image/Lh09-07.jpg diff --git a/data_images/langerhans_islets/image/Lh10-03.jpg b/data-images/langerhans_islets/image/Lh10-03.jpg similarity index 100% rename from data_images/langerhans_islets/image/Lh10-03.jpg rename to data-images/langerhans_islets/image/Lh10-03.jpg diff --git a/data_images/langerhans_islets/image/gtExoIsl_13.jpg b/data-images/langerhans_islets/image/gtExoIsl_13.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/langerhans_islets/image/gtExoIsl_13.jpg rename to data-images/langerhans_islets/image/gtExoIsl_13.jpg diff --git a/data_images/langerhans_islets/image/gtExoIsl_21.jpg b/data-images/langerhans_islets/image/gtExoIsl_21.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/langerhans_islets/image/gtExoIsl_21.jpg rename to data-images/langerhans_islets/image/gtExoIsl_21.jpg diff --git a/data_images/langerhans_islets/image/gtExoIsl_27.jpg b/data-images/langerhans_islets/image/gtExoIsl_27.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/langerhans_islets/image/gtExoIsl_27.jpg rename to data-images/langerhans_islets/image/gtExoIsl_27.jpg diff --git a/data-images/langerhans_islets/list_lang-isl_imgs-annot-2.csv b/data-images/langerhans_islets/list_lang-isl_imgs-annot-2.csv new file mode 100644 index 00000000..864a336e --- /dev/null +++ b/data-images/langerhans_islets/list_lang-isl_imgs-annot-2.csv @@ -0,0 +1,5 @@ +,path_image,path_annot +1,data-images/langerhans_islets/image/Lh05-04.jpg,data-images/langerhans_islets/annot/Lh05-04.png +2,data-images/langerhans_islets/image/Lh05-09.jpg,data-images/langerhans_islets/annot/Lh05-09.png +3,data-images/langerhans_islets/image/Lh09-07.jpg,data-images/langerhans_islets/annot/Lh09-07.png +4,data-images/langerhans_islets/image/Lh10-03.jpg,data-images/langerhans_islets/annot/Lh10-03.png diff --git a/data-images/langerhans_islets/list_lang-isl_imgs-annot.csv b/data-images/langerhans_islets/list_lang-isl_imgs-annot.csv new file mode 100644 index 00000000..2e830787 --- /dev/null +++ b/data-images/langerhans_islets/list_lang-isl_imgs-annot.csv @@ -0,0 +1,4 @@ +,path_image,path_annot +1,data-images/langerhans_islets/image/gtExoIsl_13.jpg,data-images/langerhans_islets/annot/gtExoIsl_13.png +2,data-images/langerhans_islets/image/gtExoIsl_21.jpg,data-images/langerhans_islets/annot/gtExoIsl_21.png +3,data-images/langerhans_islets/image/gtExoIsl_27.jpg,data-images/langerhans_islets/annot/gtExoIsl_27.png diff --git a/data_images/others/industry.jpg b/data-images/others/industry.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/others/industry.jpg rename to data-images/others/industry.jpg diff --git a/data_images/others/lena.png b/data-images/others/lena.png similarity index 100% rename from data_images/others/lena.png rename to data-images/others/lena.png diff --git a/data_images/others/sample.zvi b/data-images/others/sample.zvi old mode 100755 new mode 100644 similarity index 100% rename from data_images/others/sample.zvi rename to data-images/others/sample.zvi diff --git a/data_images/others/sea_starfish-1.jpg b/data-images/others/sea_starfish-1.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/others/sea_starfish-1.jpg rename to data-images/others/sea_starfish-1.jpg diff --git a/data_images/others/sea_starfish-2.jpg b/data-images/others/sea_starfish-2.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/others/sea_starfish-2.jpg rename to data-images/others/sea_starfish-2.jpg diff --git a/data_images/synthetic/moving-affine.jpg b/data-images/synthetic/moving-affine.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/moving-affine.jpg rename to data-images/synthetic/moving-affine.jpg diff --git a/data_images/synthetic/moving-elastic.jpg b/data-images/synthetic/moving-elastic.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/moving-elastic.jpg rename to data-images/synthetic/moving-elastic.jpg diff --git a/data_images/synthetic/reference.jpg b/data-images/synthetic/reference.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/reference.jpg rename to data-images/synthetic/reference.jpg diff --git a/data_images/synthetic/texture-1.jpg b/data-images/synthetic/texture-1.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/texture-1.jpg rename to data-images/synthetic/texture-1.jpg diff --git a/data_images/synthetic/texture-2_gray.jpg b/data-images/synthetic/texture-2_gray.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/texture-2_gray.jpg rename to data-images/synthetic/texture-2_gray.jpg diff --git a/data_images/synthetic/texture-3-small_annot.png b/data-images/synthetic/texture-3-small_annot.png old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/texture-3-small_annot.png rename to data-images/synthetic/texture-3-small_annot.png diff --git a/data_images/synthetic/texture-3-small_gray.jpg b/data-images/synthetic/texture-3-small_gray.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/texture-3-small_gray.jpg rename to data-images/synthetic/texture-3-small_gray.jpg diff --git a/data_images/synthetic/texture_rgb_3cls.jpg b/data-images/synthetic/texture_rgb_3cls.jpg old mode 100755 new mode 100644 similarity index 100% rename from data_images/synthetic/texture_rgb_3cls.jpg rename to data-images/synthetic/texture_rgb_3cls.jpg diff --git a/data_images/drosophila_disc/list_imaginal-disks.csv b/data_images/drosophila_disc/list_imaginal-disks.csv deleted file mode 100644 index 3e134e25..00000000 --- a/data_images/drosophila_disc/list_imaginal-disks.csv +++ /dev/null @@ -1,11 +0,0 @@ -,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 diff --git a/data_images/drosophila_disc/list_imaginal-disks_short.csv b/data_images/drosophila_disc/list_imaginal-disks_short.csv deleted file mode 100644 index 8c9248d4..00000000 --- a/data_images/drosophila_disc/list_imaginal-disks_short.csv +++ /dev/null @@ -1,3 +0,0 @@ -,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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-annot-struct.csv b/data_images/drosophila_ovary_slice/list_imgs-annot-struct.csv deleted file mode 100644 index b5645329..00000000 --- a/data_images/drosophila_ovary_slice/list_imgs-annot-struct.csv +++ /dev/null @@ -1,11 +0,0 @@ -,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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv b/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv deleted file mode 100644 index 24cc4dec..00000000 --- a/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels.csv +++ /dev/null @@ -1,6 +0,0 @@ -,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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv b/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv deleted file mode 100644 index 97455de1..00000000 --- a/data_images/drosophila_ovary_slice/list_imgs-segm-center-levels_short.csv +++ /dev/null @@ -1,3 +0,0 @@ -,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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-segm-center-points.csv b/data_images/drosophila_ovary_slice/list_imgs-segm-center-points.csv deleted file mode 100644 index 4f01a95e..00000000 --- a/data_images/drosophila_ovary_slice/list_imgs-segm-center-points.csv +++ /dev/null @@ -1,6 +0,0 @@ -,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 diff --git a/data_images/drosophila_ovary_slice/list_imgs-segm-center-points_short.csv b/data_images/drosophila_ovary_slice/list_imgs-segm-center-points_short.csv deleted file mode 100644 index bed54caf..00000000 --- a/data_images/drosophila_ovary_slice/list_imgs-segm-center-points_short.csv +++ /dev/null @@ -1,3 +0,0 @@ -,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 diff --git a/data_images/langerhans_islets/list_lang-isl_imgs-annot-2.csv b/data_images/langerhans_islets/list_lang-isl_imgs-annot-2.csv deleted file mode 100644 index 6d0a2c69..00000000 --- a/data_images/langerhans_islets/list_lang-isl_imgs-annot-2.csv +++ /dev/null @@ -1,5 +0,0 @@ -,path_image,path_annot -1,data_images/langerhans_islets/image/Lh05-04.jpg,data_images/langerhans_islets/annot/Lh05-04.png -2,data_images/langerhans_islets/image/Lh05-09.jpg,data_images/langerhans_islets/annot/Lh05-09.png -3,data_images/langerhans_islets/image/Lh09-07.jpg,data_images/langerhans_islets/annot/Lh09-07.png -4,data_images/langerhans_islets/image/Lh10-03.jpg,data_images/langerhans_islets/annot/Lh10-03.png diff --git a/data_images/langerhans_islets/list_lang-isl_imgs-annot.csv b/data_images/langerhans_islets/list_lang-isl_imgs-annot.csv deleted file mode 100644 index 63518630..00000000 --- a/data_images/langerhans_islets/list_lang-isl_imgs-annot.csv +++ /dev/null @@ -1,4 +0,0 @@ -,path_image,path_annot -1,data_images/langerhans_islets/image/gtExoIsl_13.jpg,data_images/langerhans_islets/annot/gtExoIsl_13.png -2,data_images/langerhans_islets/image/gtExoIsl_21.jpg,data_images/langerhans_islets/annot/gtExoIsl_21.png -3,data_images/langerhans_islets/image/gtExoIsl_27.jpg,data_images/langerhans_islets/annot/gtExoIsl_27.png diff --git a/docs/source/conf.py b/docs/source/conf.py index 7dd3ea80..5d6608d8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -56,15 +56,16 @@ readme = fp.read() # replace all paths to relative readme = readme.replace('](docs/source/', '](') +# Todo: this seems to replace only once per line readme = re.sub(r' \[(.*)\]\((?!http)(.*)\)', r' [\1](https://github.com/%s/%s/blob/master/\2)' % (github_user, github_repo), readme) # TODO: temp fix removing SVG badges and GIF, because PDF cannot show them readme = re.sub(r'(\[!\[.*\))', '', readme) readme = re.sub(r'(!\[.*.gif\))', '', readme) -# for dir_name in (os.path.basename(p) for p in glob.glob(os.path.join(PATH_ROOT, '*')) -# if os.path.isdir(p)): -# readme = readme.replace('](%s/' % dir_name, '](%s/%s/' % (PATH_ROOT, dir_name)) +for dir_name in (os.path.basename(p) for p in glob.glob(os.path.join(PATH_ROOT, '*')) + if os.path.isdir(p)): + readme = readme.replace('](%s/' % dir_name, '](%s/%s/' % (PATH_ROOT, dir_name)) with open('readme.md', 'w') as fp: fp.write(readme) @@ -124,7 +125,7 @@ # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = [ - 'data_images', + 'data-images', '*tests.*', '*.test_*', '*.so', '*.dll', 'modules.rst', @@ -151,7 +152,7 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_figures'] # , '_static', 'notebooks' +html_static_path = [] # , '_static', 'notebooks' # Custom sidebar templates, must be a dictionary that maps document names # to template names. diff --git a/experiments_ovary_centres/gui_annot_center_correction.py b/experiments_ovary_centres/gui_annot_center_correction.py index 587c53c6..4f6e7244 100755 --- a/experiments_ovary_centres/gui_annot_center_correction.py +++ b/experiments_ovary_centres/gui_annot_center_correction.py @@ -51,7 +51,7 @@ import imsegm.utilities.data_io as tl_data import imsegm.utilities.drawing as tl_visu -PATH_BASE = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_BASE = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) PATH_IMAGES = os.path.join(PATH_BASE, 'image', '*.jpg') PATH_CSV = os.path.join(PATH_BASE, 'center_levels', '*.csv') NAME_INFO_SHORT = 'ovary_image_info.csv' diff --git a/experiments_ovary_centres/run_center_candidate_training.py b/experiments_ovary_centres/run_center_candidate_training.py index 61db0dd3..b2caebb5 100755 --- a/experiments_ovary_centres/run_center_candidate_training.py +++ b/experiments_ovary_centres/run_center_candidate_training.py @@ -16,9 +16,9 @@ Sample usage:: python run_center_candidate_training.py -list none \ - -imgs "data_images/drosophila_ovary_slice/image/*.jpg" \ - -segs "data_images/drosophila_ovary_slice/segm/*.png" \ - -centers "data_images/drosophila_ovary_slice/center_levels/*.png" \ + -imgs "data-images/drosophila_ovary_slice/image/*.jpg" \ + -segs "data-images/drosophila_ovary_slice/segm/*.png" \ + -centers "data-images/drosophila_ovary_slice/center_levels/*.png" \ -out results -n ovary Copyright (C) 2016-2017 Jiri Borovec @@ -102,7 +102,7 @@ 'center_dist_thr': 50, # distance to from annotated center as a point } -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_RESULTS = tl_data.update_path('results', absolute=True) CENTER_PARAMS.update({ diff --git a/experiments_ovary_centres/run_center_evaluation.py b/experiments_ovary_centres/run_center_evaluation.py index a3341495..594ad260 100755 --- a/experiments_ovary_centres/run_center_evaluation.py +++ b/experiments_ovary_centres/run_center_evaluation.py @@ -5,8 +5,8 @@ Sample usage:: python run_center_evaluation.py -list none \ - -segs "data_images/drosophila_ovary_slice/segm/*.png" \ - -imgs "data_images/drosophila_ovary_slice/image/*.jpg" \ + -segs "data-images/drosophila_ovary_slice/segm/*.png" \ + -imgs "data-images/drosophila_ovary_slice/image/*.jpg" \ -centers "results/detect-centers-predict_ovary/centers/*.csv" \ -out results/detect-centers-predict_ovary diff --git a/experiments_ovary_centres/run_center_prediction.py b/experiments_ovary_centres/run_center_prediction.py index 35447e2e..8c105f33 100644 --- a/experiments_ovary_centres/run_center_prediction.py +++ b/experiments_ovary_centres/run_center_prediction.py @@ -5,8 +5,8 @@ Sample usage:: python run_center_prediction.py -list none \ - -segs "data_images/drosophila_ovary_slice/segm/*.png" \ - -imgs "data_images/drosophila_ovary_slice/image/*.jpg" \ + -segs "data-images/drosophila_ovary_slice/segm/*.png" \ + -imgs "data-images/drosophila_ovary_slice/image/*.jpg" \ -centers results/detect-centers-train_ovary/classifier_RandForest.pkl \ -out results -n ovary diff --git a/experiments_ovary_detect/run_RG2Sp_estim_shape-models.py b/experiments_ovary_detect/run_RG2Sp_estim_shape-models.py index 45df8c8f..93a050cb 100644 --- a/experiments_ovary_detect/run_RG2Sp_estim_shape-models.py +++ b/experiments_ovary_detect/run_RG2Sp_estim_shape-models.py @@ -24,8 +24,8 @@ import imsegm.utilities.data_io as tl_data import imsegm.region_growing as tl_rg -PATH_DATA = tl_data.update_path('data_images', absolute=True) -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), 'drosophila_ovary_slice') +PATH_DATA = tl_data.update_path('data-images', absolute=True) +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_ANNOT = os.path.join(PATH_IMAGES, 'annot_eggs', '*.png') RAY_STEP = 10 # names of default files for models diff --git a/experiments_ovary_detect/run_cut_segmented_objects.py b/experiments_ovary_detect/run_cut_segmented_objects.py index 7936733d..7d7a126a 100644 --- a/experiments_ovary_detect/run_cut_segmented_objects.py +++ b/experiments_ovary_detect/run_cut_segmented_objects.py @@ -4,8 +4,8 @@ Sample usage:: python run_cut_segmented_objects.py \ - -annot "data_images/drosophila_ovary_slice/annot_eggs/*.png" \ - -img "data_images/drosophila_ovary_slice/segm/*.png" \ + -annot "data-images/drosophila_ovary_slice/annot_eggs/*.png" \ + -img "data-images/drosophila_ovary_slice/segm/*.png" \ -out results/cut_images --padding 20 """ @@ -23,7 +23,7 @@ import imsegm.utilities.experiments as tl_expt NB_WORKERS = tl_expt.nb_workers(0.9) -PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) PATH_RESULTS = tl_data.update_path('results', absolute=True) PATHS = { 'annot': os.path.join(PATH_IMAGES, 'annot_eggs', '*.png'), diff --git a/experiments_ovary_detect/run_egg_swap_orientation.py b/experiments_ovary_detect/run_egg_swap_orientation.py index ac628f50..d741d7a5 100644 --- a/experiments_ovary_detect/run_egg_swap_orientation.py +++ b/experiments_ovary_detect/run_egg_swap_orientation.py @@ -26,7 +26,7 @@ IMAGE_CHANNEL = 0 # image channel for mass extraction NB_WORKERS = tl_expt.nb_workers(0.8) -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_RESULTS = tl_data.update_path('results', absolute=True) SWAP_CONDITION = 'cc' diff --git a/experiments_ovary_detect/run_ellipse_annot_match.py b/experiments_ovary_detect/run_ellipse_annot_match.py index 410ca128..2e1e96fc 100644 --- a/experiments_ovary_detect/run_ellipse_annot_match.py +++ b/experiments_ovary_detect/run_ellipse_annot_match.py @@ -33,7 +33,7 @@ OVERLAP_THRESHOLD = 0. NB_WORKERS = tl_expt.nb_workers(0.8) -PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) DEFAULT_PARAMS = { 'path_ellipses': os.path.join(PATH_IMAGES, 'ellipse_fitting', '*.csv'), diff --git a/experiments_ovary_detect/run_ellipse_cut_scale.py b/experiments_ovary_detect/run_ellipse_cut_scale.py index 76609487..e35cc23b 100644 --- a/experiments_ovary_detect/run_ellipse_cut_scale.py +++ b/experiments_ovary_detect/run_ellipse_cut_scale.py @@ -34,7 +34,7 @@ NORM_FUNC = np.median # other options - mean, max, ... NB_WORKERS = tl_expt.nb_workers(0.8) -PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) PATH_RESULTS = tl_data.update_path('results', absolute=True) DEFAULT_PARAMS = { diff --git a/experiments_ovary_detect/run_export_user-annot-segm.py b/experiments_ovary_detect/run_export_user-annot-segm.py index f1a1af54..ed354431 100644 --- a/experiments_ovary_detect/run_export_user-annot-segm.py +++ b/experiments_ovary_detect/run_export_user-annot-segm.py @@ -38,7 +38,7 @@ import imsegm.annotation as seg_annot NB_WORKERS = tl_expt.nb_workers(0.8) -PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) PATH_RESULTS = tl_data.update_path('results', absolute=True) DEFAULT_PARAMS = { 'path_images': os.path.join(PATH_IMAGES, 'image', '*.jpg'), diff --git a/experiments_ovary_detect/run_ovary_egg-segmentation.py b/experiments_ovary_detect/run_ovary_egg-segmentation.py index 70910a08..ee3d9049 100755 --- a/experiments_ovary_detect/run_ovary_egg-segmentation.py +++ b/experiments_ovary_detect/run_ovary_egg-segmentation.py @@ -8,7 +8,7 @@ Sample usage:: python run_ovary_egg-segmentation.py \ - -list data_images/drosophila_ovary_slice/list_imgs-segm-center-points.csv \ + -list data-images/drosophila_ovary_slice/list_imgs-segm-center-points.csv \ -out results -n ovary_slices --nb_workers 1 \ -m ellipse_moments \ ellipse_ransac_mmt \ @@ -92,7 +92,7 @@ } COLUMNS_ELLIPSE = ('xc', 'yc', 'a', 'b', 'theta') -PATH_DATA = tl_data.update_path('data_images', absolute=True) +PATH_DATA = tl_data.update_path('data-images', absolute=True) PATH_IMAGES = os.path.join(PATH_DATA, 'drosophila_ovary_slice') # sample segmentation methods LIST_SAMPLE_METHODS = ( diff --git a/experiments_ovary_detect/run_ovary_segm_evaluation.py b/experiments_ovary_detect/run_ovary_segm_evaluation.py index 6fe0c43d..6a7d14fa 100755 --- a/experiments_ovary_detect/run_ovary_segm_evaluation.py +++ b/experiments_ovary_detect/run_ovary_segm_evaluation.py @@ -46,7 +46,7 @@ SKIP_DIRS = ['input', 'simple', NAME_DIR_VISUAL_1, NAME_DIR_VISUAL_2, NAME_DIR_VISUAL_3] NAME_CSV_STAT = 'segmented-eggs_%s.csv' -PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'drosophila_ovary_slice')) +PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'drosophila_ovary_slice')) PATH_RESULTS = tl_data.update_path('results', absolute=True) PATHS = { 'images': os.path.join(PATH_IMAGES, 'image', '*.jpg'), diff --git a/experiments_segmentation/run_compute_stat_annot_segm.py b/experiments_segmentation/run_compute_stat_annot_segm.py index 5c48f624..e0002056 100644 --- a/experiments_segmentation/run_compute_stat_annot_segm.py +++ b/experiments_segmentation/run_compute_stat_annot_segm.py @@ -5,9 +5,9 @@ Sample usage:: python run_compute_stat_annot_segm.py \ - -a "data_images/drosophila_ovary_slice/annot_struct/*.png" \ + -a "data-images/drosophila_ovary_slice/annot_struct/*.png" \ -s "results/experiment_segm-supervise_ovary/*.png" \ - -i "data_images/drosophila_ovary_slice/image/*.jpg" \ + -i "data-images/drosophila_ovary_slice/image/*.jpg" \ -o results/evaluation --drop_labels -1 --overlap 0.2 --visual Copyright (C) 2016-2018 Jiri Borovec @@ -39,7 +39,7 @@ NB_WORKERS = tl_expt.nb_workers(0.9) NAME_CVS_OVERALL = 'STATISTIC__%s___Overall.csv' NAME_CVS_PER_IMAGE = 'STATISTIC__%s___per-Image.csv' -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_RESULTS = tl_data.update_path('results', absolute=True) SUFFIX_VISUAL = '___STAT-visual' diff --git a/experiments_segmentation/run_eval_superpixels.py b/experiments_segmentation/run_eval_superpixels.py index cb4e2f7d..9dd0f85e 100644 --- a/experiments_segmentation/run_eval_superpixels.py +++ b/experiments_segmentation/run_eval_superpixels.py @@ -6,8 +6,8 @@ Sample usage:: python run_eval_superpixels.py \ - -imgs "data_images/drosophila_ovary_slice/image/*.jpg" \ - -segm "data_images/drosophila_ovary_slice/annot_eggs/*.png" \ + -imgs "data-images/drosophila_ovary_slice/image/*.jpg" \ + -segm "data-images/drosophila_ovary_slice/annot_eggs/*.png" \ --img_type 2d_split \ --slic_size 20 --slic_regul 0.25 --slico @@ -41,7 +41,7 @@ NB_WORKERS = tl_expt.nb_workers(0.9) -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_RESULTS = tl_data.update_path('results', absolute=True) NAME_CSV_DISTANCES = 'measured_boundary_distances' \ diff --git a/experiments_segmentation/run_segm_slic_classif_graphcut.py b/experiments_segmentation/run_segm_slic_classif_graphcut.py index 382b7385..ea70418c 100644 --- a/experiments_segmentation/run_segm_slic_classif_graphcut.py +++ b/experiments_segmentation/run_segm_slic_classif_graphcut.py @@ -20,8 +20,8 @@ Sample usage:: python run_segm_slic_classif_graphcut.py \ - -l data_images/drosophila_ovary_slice/list_imgs-annot-struct.csv \ - -i "data_images/drosophila_ovary_slice/image/*.jpg" \ + -l data-images/drosophila_ovary_slice/list_imgs-annot-struct.csv \ + -i "data-images/drosophila_ovary_slice/image/*.jpg" \ --path_config experiments_segmentation/sample_config.yml \ -o results -n Ovary --img_type 2d_split --visual @@ -136,7 +136,7 @@ 'gc_edge_type': 'model', 'gc_use_trans': False, } -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice') PATH_RESULTS = tl_data.update_path('results', absolute=True) SEGM_PARAMS.update({ diff --git a/experiments_segmentation/run_segm_slic_model_graphcut.py b/experiments_segmentation/run_segm_slic_model_graphcut.py index 556d58e9..99a324bc 100644 --- a/experiments_segmentation/run_segm_slic_model_graphcut.py +++ b/experiments_segmentation/run_segm_slic_model_graphcut.py @@ -14,8 +14,8 @@ Sample usage:: python run_segm_slic_model_graphcut.py \ - -l data_images/langerhans_islets/list_lang-isl_imgs-annot.csv \ - -i "data_images/langerhans_islets/image/*.jpg" \ + -l data-images/langerhans_islets/list_lang-isl_imgs-annot.csv \ + -i "data-images/langerhans_islets/image/*.jpg" \ -o results -n LangIsl --nb_classes 3 --nb_workers 2 --visual Copyright (C) 2016-2018 Jiri Borovec @@ -103,8 +103,8 @@ 'gc_edge_type': 'model', 'gc_use_trans': False, } -PATH_IMAGES = os.path.join(tl_data.update_path('data_images'), 'drosophila_disc') -# PATH_IMAGES = tl_data.update_path(os.path.join('data_images', 'langerhans_islets')) +PATH_IMAGES = os.path.join(tl_data.update_path('data-images'), 'drosophila_disc') +# PATH_IMAGES = tl_data.update_path(os.path.join('data-images', 'langerhans_islets')) PATH_RESULTS = tl_data.update_path('results', absolute=True) NAME_EXPERIMENT = 'experiment_segm-unSupervised' SEGM_PARAMS.update({ diff --git a/experiments_segmentation/test_segmentations.sh b/experiments_segmentation/test_segmentations.sh index 1e811bfb..11ffdeb1 100644 --- a/experiments_segmentation/test_segmentations.sh +++ b/experiments_segmentation/test_segmentations.sh @@ -2,15 +2,15 @@ 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" \ + -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" \ + -i "data-images/drosophila_disc/image/img_[5,6].jpg" \ -cfg ./experiments_segmentation/sample_config.yml \ --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" \ + -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.yml \ --visual \ No newline at end of file diff --git a/handling_annotations/run_image_color_quantization.py b/handling_annotations/run_image_color_quantization.py index 17448048..d04b6e9b 100644 --- a/handling_annotations/run_image_color_quantization.py +++ b/handling_annotations/run_image_color_quantization.py @@ -9,7 +9,7 @@ SAMPLE run:: python run_image_color_quantization.py \ - -imgs "data_images/drosophila_ovary_slice/segm_rgb/*.png" \ + -imgs "data-images/drosophila_ovary_slice/segm_rgb/*.png" \ -m position Copyright (C) 2014-2016 Jiri Borovec @@ -30,7 +30,7 @@ import imsegm.utilities.experiments as tl_expt import imsegm.annotation as seg_annot -PATH_IMAGES = os.path.join('data_images', 'drosophila_ovary_slice', 'segm_rgb', '*.png') +PATH_IMAGES = os.path.join('data-images', 'drosophila_ovary_slice', 'segm_rgb', '*.png') NB_WORKERS = tl_expt.nb_workers(0.9) THRESHOLD_INVALID_PIXELS = 5e-3 diff --git a/handling_annotations/run_image_convert_label_color.py b/handling_annotations/run_image_convert_label_color.py index ae00e401..4ff35a92 100644 --- a/handling_annotations/run_image_convert_label_color.py +++ b/handling_annotations/run_image_convert_label_color.py @@ -4,9 +4,9 @@ SAMPLE run:: python run_image_convert_label_color.py \ - -imgs "data_images/drosophila_ovary_slice/segm/*.png" \ - -out data_images/drosophila_ovary_slice/segm_rgb \ - -clrs data_images/drosophila_ovary_slice/segm_rgb/dict_label-color.json + -imgs "data-images/drosophila_ovary_slice/segm/*.png" \ + -out data-images/drosophila_ovary_slice/segm_rgb \ + -clrs data-images/drosophila_ovary_slice/segm_rgb/dict_label-color.json Copyright (C) 2014-2016 Jiri Borovec """ @@ -27,8 +27,8 @@ import imsegm.utilities.experiments as tl_expt import imsegm.annotation as seg_annot -PATH_INPUT = os.path.join('data_images', 'drosophila_ovary_slice', 'segm', '*.png') -PATH_OUTPUT = os.path.join('data_images', 'drosophila_ovary_slice', 'segm_rgb') +PATH_INPUT = os.path.join('data-images', 'drosophila_ovary_slice', 'segm', '*.png') +PATH_OUTPUT = os.path.join('data-images', 'drosophila_ovary_slice', 'segm_rgb') NAME_JSON_DICT = 'dictionary_label-color.json' NB_WORKERS = tl_expt.nb_workers(0.9) diff --git a/handling_annotations/run_overlap_images_segms.py b/handling_annotations/run_overlap_images_segms.py index 54c78bf5..e5150f9e 100644 --- a/handling_annotations/run_overlap_images_segms.py +++ b/handling_annotations/run_overlap_images_segms.py @@ -5,8 +5,8 @@ SAMPLE run:: python run_overlap_images_segms.py \ - -imgs "data_images/drosophila_ovary_slice/image/*.jpg" \ - -segs data_images/drosophila_ovary_slice/segm \ + -imgs "data-images/drosophila_ovary_slice/image/*.jpg" \ + -segs data-images/drosophila_ovary_slice/segm \ -out results/overlap_ovary_segment Copyright (C) 2014-2016 Jiri Borovec diff --git a/handling_annotations/run_segm_annot_inpaint.py b/handling_annotations/run_segm_annot_inpaint.py index 9e1a383a..198f273f 100644 --- a/handling_annotations/run_segm_annot_inpaint.py +++ b/handling_annotations/run_segm_annot_inpaint.py @@ -4,7 +4,7 @@ SAMPLE run:: python run_image_annot_inpaint.py \ - -imgs "data_images/drosophila_ovary_slice/segm/*.png" \ + -imgs "data-images/drosophila_ovary_slice/segm/*.png" \ --label 4 --nb_workers 2 Copyright (C) 2014-2016 Jiri Borovec @@ -25,7 +25,7 @@ import imsegm.utilities.experiments as tl_expt import imsegm.annotation as seg_annot -PATH_IMAGES = os.path.join('data_images', 'drosophila_ovary_slice', 'segm', '*.png') +PATH_IMAGES = os.path.join('data-images', 'drosophila_ovary_slice', 'segm', '*.png') NB_WORKERS = tl_expt.nb_workers(0.9) diff --git a/handling_annotations/run_segm_annot_relabel.py b/handling_annotations/run_segm_annot_relabel.py index 247230bd..a1bf5173 100644 --- a/handling_annotations/run_segm_annot_relabel.py +++ b/handling_annotations/run_segm_annot_relabel.py @@ -4,7 +4,7 @@ SAMPLE run:: python run_segm_annot_relabel.py \ - -imgs "data_images/drosophila_ovary_slice/center_levels/*.png" \ + -imgs "data-images/drosophila_ovary_slice/center_levels/*.png" \ -out results/relabel_center_levels \ --label_old 2 3 --label_new 1 1 --nb_workers 2 @@ -25,7 +25,7 @@ import imsegm.utilities.data_io as tl_data import imsegm.utilities.experiments as tl_expt -PATH_IMAGES = os.path.join('data_images', 'drosophila_ovary_slice', 'center_levels', '*.png') +PATH_IMAGES = os.path.join('data-images', 'drosophila_ovary_slice', 'center_levels', '*.png') PATH_OUTPUT = os.path.join('results', 'relabel_center_levels') NB_WORKERS = tl_expt.nb_workers(0.9) diff --git a/handling_annotations/test_annotations.sh b/handling_annotations/test_annotations.sh index d9cc2206..fd690243 100644 --- a/handling_annotations/test_annotations.sh +++ b/handling_annotations/test_annotations.sh @@ -1,23 +1,23 @@ #!/usr/bin/env bash python handling_annotations/run_image_color_quantization.py \ - -imgs "./data_images/drosophila_ovary_slice/segm_rgb/*.png" + -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" \ + -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 + -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 + -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 \ + -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" \ + -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" \ + -imgs "./data-images/drosophila_ovary_slice/center_levels/*.png" \ -out ./results/relabel_center_levels \ No newline at end of file diff --git a/imsegm/__init__.py b/imsegm/__init__.py index 7d8d6709..93f84b9c 100755 --- a/imsegm/__init__.py +++ b/imsegm/__init__.py @@ -16,7 +16,7 @@ __author_email__ = 'jiri.borovec@fel.cvut.cz' __license__ = 'BSD 3-clause' __homepage__ = 'https://borda.github.io/pyImSegm' -__copyright__ = 'Copyright (c) 2014-2019, %s.' % __author__ +__copyright__ = 'Copyright (c) 2014-2020, %s.' % __author__ __doc__ = 'Image segmentation - general superpixel segmentation & region growing' __long_doc__ = "# %s" % __doc__ + """ diff --git a/imsegm/annotation.py b/imsegm/annotation.py index 9e78680b..79b93fec 100755 --- a/imsegm/annotation.py +++ b/imsegm/annotation.py @@ -334,7 +334,7 @@ def load_info_group_by_slices(path_txt, stages, pos_columns=COLUMNS_POSITION, :return: DF >>> from imsegm.utilities.data_io import update_path - >>> path_txt = os.path.join(update_path('data_images'), + >>> path_txt = os.path.join(update_path('data-images'), ... 'drosophila_ovary_slice', 'info_ovary_images.txt') >>> load_info_group_by_slices(path_txt, [4]) # doctest: +NORMALIZE_WHITESPACE ant_x ant_y lat_x lat_y post_x post_y diff --git a/imsegm/utilities/data_io.py b/imsegm/utilities/data_io.py index 648bcda0..d9261bea 100644 --- a/imsegm/utilities/data_io.py +++ b/imsegm/utilities/data_io.py @@ -638,12 +638,12 @@ def load_image_tiff_volume(path_img, im_range=None): :param float im_range: range to scale image values (1. or 255) :return ndarray: - >>> p_img = os.path.join(update_path('data_images'), 'drosophila_ovary_3D', + >>> p_img = os.path.join(update_path('data-images'), 'drosophila_ovary_3D', ... 'AU10-13_f0011.tif') >>> img = load_image_tiff_volume(p_img) >>> img.shape (30, 323, 512) - >>> p_img = os.path.join(update_path('data_images'), + >>> p_img = os.path.join(update_path('data-images'), ... 'drosophila_ovary_slice', 'image', 'insitu7545.tif') >>> img = load_image_tiff_volume(p_img) >>> img.shape @@ -675,12 +675,12 @@ def load_tiff_volume_split_double_band(path_img, im_range=None): :param float im_range: range to scale image values (1. or 255) :return ndarray, ndarray: - >>> p_img = os.path.join(update_path('data_images'), 'drosophila_ovary_3D', + >>> p_img = os.path.join(update_path('data-images'), 'drosophila_ovary_3D', ... 'AU10-13_f0011.tif') >>> img_b1, img_b2 = load_tiff_volume_split_double_band(p_img) >>> img_b1.shape, img_b2.shape ((15, 323, 512), (15, 323, 512)) - >>> p_img = os.path.join(update_path('data_images'), + >>> p_img = os.path.join(update_path('data-images'), ... 'drosophila_ovary_slice', 'image', 'insitu7545.tif') >>> img_b1, img_b2 = load_tiff_volume_split_double_band(p_img) >>> img_b1.shape, img_b2.shape @@ -722,7 +722,7 @@ def load_zvi_volume_double_band_split(path_img): :param str path_img: path to the image :return ndarray, ndarray: - >>> p_img = os.path.join(update_path('data_images'), 'others', 'sample.zvi') + >>> p_img = os.path.join(update_path('data-images'), 'others', 'sample.zvi') >>> img_b1, img_b2 = load_zvi_volume_double_band_split(p_img) >>> img_b1.shape (2, 488, 648) @@ -743,7 +743,7 @@ def load_img_double_band_split(path_img, im_range=1., quantiles=(2, 98)): :param tuple(int,int) quantiles: scale image values in certain percentile range :return: - >>> p_imgs = os.path.join(update_path('data_images'), 'drosophila_ovary_slice', 'image') + >>> p_imgs = os.path.join(update_path('data-images'), 'drosophila_ovary_slice', 'image') >>> p_img = os.path.join(p_imgs, 'insitu7545.jpg') >>> img_b1, img_b2 = load_img_double_band_split(p_img) >>> img_b1.shape @@ -752,7 +752,7 @@ def load_img_double_band_split(path_img, im_range=1., quantiles=(2, 98)): >>> img_b1, img_b2 = load_img_double_band_split(p_img) >>> img_b1.shape (647, 1024) - >>> p_img = os.path.join(update_path('data_images'), + >>> p_img = os.path.join(update_path('data-images'), ... 'drosophila_ovary_3D', 'AU10-13_f0011.tif') >>> img_b1, img_b2 = load_img_double_band_split(p_img) >>> img_b1.shape @@ -814,7 +814,7 @@ def load_complete_image_folder(path_dir, img_name_pattern='*.png', :param list(str)|None skip: skip some prticular images by name :return: - >>> p_imgs = os.path.join(update_path('data_images'), + >>> p_imgs = os.path.join(update_path('data-images'), ... 'drosophila_ovary_slice', 'image') >>> l_imgs, l_names = load_complete_image_folder(p_imgs, '*.jpg') >>> len(l_imgs) @@ -934,7 +934,7 @@ def find_files_match_names_across_dirs(list_path_pattern, drop_none=True): :return: DF >>> def _mp(d, n): - ... return os.path.join(update_path('data_images'), + ... return os.path.join(update_path('data-images'), ... 'drosophila_ovary_slice', d, n) >>> df = find_files_match_names_across_dirs([_mp('image', '*.jpg'), ... _mp('segm', '*.png'), diff --git a/imsegm/utilities/data_samples.py b/imsegm/utilities/data_samples.py index 240bfde3..8bd0daa2 100644 --- a/imsegm/utilities/data_samples.py +++ b/imsegm/utilities/data_samples.py @@ -28,7 +28,7 @@ SAMPLE_SEG_SIZE_3D_SMALL = (10, 5, 6) #: path to the folder with all sample image/data -PATH_IMAGES = update_path('data_images') +PATH_IMAGES = update_path('data-images') #: sample Lenna image IMAGE_LENNA = os.path.join('others', 'lena.png') #: sample image with three color objects of different shape diff --git a/imsegm/utilities/read_zvi.py b/imsegm/utilities/read_zvi.py index a5187362..702f40d2 100644 --- a/imsegm/utilities/read_zvi.py +++ b/imsegm/utilities/read_zvi.py @@ -14,7 +14,7 @@ >>> import os, sys >>> sys.path += [os.path.abspath(os.path.join('..', '..'))] >>> import imsegm.utilities.data_io as tl_io ->>> path_file = os.path.join('data_images', 'others', 'sample.zvi') +>>> path_file = os.path.join('data-images', 'others', 'sample.zvi') >>> path_file = tl_io.update_path(path_file) >>> n = get_layer_count(path_file) >>> get_dir(path_file) # doctest: +ELLIPSIS diff --git a/notebooks/RG2Sp_model_region-grow.ipynb b/notebooks/RG2Sp_model_region-grow.ipynb index 3c103dac..b90154a1 100755 --- a/notebooks/RG2Sp_model_region-grow.ipynb +++ b/notebooks/RG2Sp_model_region-grow.ipynb @@ -80,8 +80,8 @@ ], "source": [ "COLORS = 'bgrmyck'\n", - "PATH_IMAGES = os.path.join(tl_io.update_path('data_images'), 'langerhans_islets')\n", - "PATH_DATA = tl_io.update_path('data_images', absolute=True)\n", + "PATH_IMAGES = os.path.join(tl_io.update_path('data-images'), 'langerhans_islets')\n", + "PATH_DATA = tl_io.update_path('data-images', absolute=True)\n", "PATH_OUT = tl_io.update_path('output', absolute=True)\n", "PATH_MEASURED_RAYS = os.path.join(PATH_IMAGES, 'islets_ray-shapes_1400x1050.csv')\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(PATH_IMAGES, '*')) if os.path.isdir(p)])\n", diff --git a/notebooks/RG2Sp_region-growing.ipynb b/notebooks/RG2Sp_region-growing.ipynb index 3f2983b0..659b5d85 100755 --- a/notebooks/RG2Sp_region-growing.ipynb +++ b/notebooks/RG2Sp_region-growing.ipynb @@ -77,8 +77,8 @@ "source": [ "COLORS = 'bgrmyck'\n", "RG2SP_THRESHOLDS = seg_rg.RG2SP_THRESHOLDS\n", - "PATH_IMAGES = os.path.join(tl_io.update_path('data_images'), 'drosophila_ovary_slice')\n", - "PATH_DATA = tl_io.update_path('data_images', absolute=True)\n", + "PATH_IMAGES = os.path.join(tl_io.update_path('data-images'), 'drosophila_ovary_slice')\n", + "PATH_DATA = tl_io.update_path('data-images', absolute=True)\n", "PATH_OUT = tl_io.update_path('output', absolute=True)\n", "PATH_MEASURED_RAYS = os.path.join(PATH_IMAGES, 'eggs_ray-shapes.csv')\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(PATH_IMAGES, '*')) if os.path.isdir(p)])" diff --git a/notebooks/RG2Sp_shape-models.ipynb b/notebooks/RG2Sp_shape-models.ipynb index 4fc7b436..af68d00a 100755 --- a/notebooks/RG2Sp_shape-models.ipynb +++ b/notebooks/RG2Sp_shape-models.ipynb @@ -72,8 +72,8 @@ ], "source": [ "COLORS = 'bgrmyck'\n", - "PATH_IMAGES = tl_io.update_path(os.path.join('data_images', 'drosophila_ovary_slice'))\n", - "PATH_DATA = tl_io.update_path('data_images', absolute=True)\n", + "PATH_IMAGES = tl_io.update_path(os.path.join('data-images', 'drosophila_ovary_slice'))\n", + "PATH_DATA = tl_io.update_path('data-images', absolute=True)\n", "PATH_OUT = tl_io.update_path('output', absolute=True)\n", "PATH_MEASURED_RAYS = os.path.join(PATH_IMAGES, 'eggs_ray-shapes.csv')\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(PATH_IMAGES, '*')) if os.path.isdir(p)])\n", diff --git a/notebooks/egg-center_candidates-clustering.ipynb b/notebooks/egg-center_candidates-clustering.ipynb index 84342a02..75b7a1af 100644 --- a/notebooks/egg-center_candidates-clustering.ipynb +++ b/notebooks/egg-center_candidates-clustering.ipynb @@ -78,7 +78,7 @@ "outputs": [], "source": [ "name = 'insitu7545'\n", - "PATH_BASE = tl_io.update_path(os.path.join('data_images', 'drosophila_ovary_slice'))\n", + "PATH_BASE = tl_io.update_path(os.path.join('data-images', 'drosophila_ovary_slice'))\n", "PATH_IMAGES = os.path.join(PATH_BASE, 'image')\n", "PATH_SEGM = os.path.join(PATH_BASE, 'segm')\n", "PATH_ANNOT = os.path.join(PATH_BASE, 'annot_eggs')\n", diff --git a/notebooks/egg-detect_ellipse-fitting.ipynb b/notebooks/egg-detect_ellipse-fitting.ipynb index 21933512..6c7752cc 100755 --- a/notebooks/egg-detect_ellipse-fitting.ipynb +++ b/notebooks/egg-detect_ellipse-fitting.ipynb @@ -74,7 +74,7 @@ }, "outputs": [], "source": [ - "PATH_BASE = tl_io.update_path(os.path.join('data_images', 'drosophila_ovary_slice'))\n", + "PATH_BASE = tl_io.update_path(os.path.join('data-images', 'drosophila_ovary_slice'))\n", "PATH_IMAGES = os.path.join(PATH_BASE, 'image')\n", "PATH_SEGM = os.path.join(PATH_BASE, 'segm')\n", "PATH_ANNOT = os.path.join(PATH_BASE, 'annot_eggs')\n", diff --git a/notebooks/egg_segment_graphcut.ipynb b/notebooks/egg_segment_graphcut.ipynb index 4621a2fa..da4f7ad6 100755 --- a/notebooks/egg_segment_graphcut.ipynb +++ b/notebooks/egg_segment_graphcut.ipynb @@ -72,7 +72,7 @@ ], "source": [ "COLORS = 'bgrmyck'\n", - "PATH_IMAGES = tl_io.update_path(os.path.join('data_images', 'drosophila_ovary_slice'))\n", + "PATH_IMAGES = tl_io.update_path(os.path.join('data-images', 'drosophila_ovary_slice'))\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(PATH_IMAGES, '*')) if os.path.isdir(p)])\n", "dir_img = os.path.join(PATH_IMAGES, 'image')\n", "dir_segm = os.path.join(PATH_IMAGES, 'segm')\n", diff --git a/notebooks/segment-2d_slic-fts-classif-gc.ipynb b/notebooks/segment-2d_slic-fts-classif-gc.ipynb index b6e718f2..39e90a9b 100755 --- a/notebooks/segment-2d_slic-fts-classif-gc.ipynb +++ b/notebooks/segment-2d_slic-fts-classif-gc.ipynb @@ -58,7 +58,7 @@ } ], "source": [ - "path_dir = os.path.join(tl_data.update_path('data_images'), 'drosophila_ovary_slice')\n", + "path_dir = os.path.join(tl_data.update_path('data-images'), 'drosophila_ovary_slice')\n", "path_images = os.path.join(path_dir, 'image')\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(path_images, '*.jpg'))])\n", "# loading images\n", diff --git a/notebooks/segment-2d_slic-fts-clust-gc.ipynb b/notebooks/segment-2d_slic-fts-clust-gc.ipynb index 27a3f84a..2f1b2b79 100644 --- a/notebooks/segment-2d_slic-fts-clust-gc.ipynb +++ b/notebooks/segment-2d_slic-fts-clust-gc.ipynb @@ -68,7 +68,7 @@ } ], "source": [ - "path_dir = os.path.join(tl_data.update_path('data_images'), 'others')\n", + "path_dir = os.path.join(tl_data.update_path('data-images'), 'others')\n", "print ([os.path.basename(p) for p in glob.glob(os.path.join(path_dir, '*.jpg'))])\n", "path_img = os.path.join(path_dir, 'sea_starfish-2.jpg')\n", "\n", diff --git a/notebooks/transform-img-plane_inter-circle.ipynb b/notebooks/transform-img-plane_inter-circle.ipynb index 587e2254..ef15b15e 100755 --- a/notebooks/transform-img-plane_inter-circle.ipynb +++ b/notebooks/transform-img-plane_inter-circle.ipynb @@ -43,7 +43,7 @@ } ], "source": [ - "path_image = os.path.abspath(os.path.join('data_images', 'other', 'industry.jpg'))\n", + "path_image = os.path.abspath(os.path.join('data-images', 'other', 'industry.jpg'))\n", "img = Image.open(path_image)\n", "img = img.resize((int(img.width * 0.5), int(img.height * 0.5)), Image.ANTIALIAS)\n", "img = np.array(img)\n", diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index bb385a74..00000000 --- a/pytest.ini +++ /dev/null @@ -1,11 +0,0 @@ -[pytest] -log_cli = 1 -log_cli_level = CRITICAL -log_cli_format = %(message)s - -log_file = pytest.log -log_file_level = DEBUG -log_file_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s) -log_file_date_format=%Y-%m-%d %H:%M:%S - -filterwarnings = ignore::FutureWarning \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index fb780da5..f0e8d817 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,5 +10,25 @@ requirements-file = requirements.txt # http://flake8.pycqa.org/en/latest/user/configuration.html ignore = E402,E731 max-line-length = 100 -# exclude = tests/* -# max-complexity = 10 \ No newline at end of file +exclude = .tox,*.egg,build,temp +select = E,W,F +doctests = True +verbose = 2 +# max-complexity = 10 + +[tool:pytest] +log_cli = 1 +log_cli_level = CRITICAL +log_cli_format = %(message)s +log_file = pytest.log +log_file_level = DEBUG +log_file_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s) +log_file_date_format=%Y-%m-%d %H:%M:%S +filterwarnings = ignore::FutureWarning + +[pydocstyle] +convention = pep257 +# D104, D107: Ignore missing docstrings in __init__ files and methods. +# D202: Ignore a blank line after docstring (collision with Python Black in decorators) +add-ignore = D104,D107,D202 +max-line-length = 120 diff --git a/tests/test_descriptors.py b/tests/test_descriptors.py index d72b61d7..ddb437a3 100644 --- a/tests/test_descriptors.py +++ b/tests/test_descriptors.py @@ -33,7 +33,7 @@ PATH_FIGURES_RAY = os.path.join(PATH_OUTPUT, 'temp_ray-features') # create the folder for visualisations if not os.path.exists(PATH_FIGURES_RAY): - os.mkdir(PATH_FIGURES_RAY) + os.makedirs(PATH_FIGURES_RAY, exist_ok=True) def export_ray_results(seg, center, points, ray_dist_raw, ray_dist, name): diff --git a/tests/test_ellipse-fitting.py b/tests/test_ellipse-fitting.py index 375c76a6..8c2b6eee 100644 --- a/tests/test_ellipse-fitting.py +++ b/tests/test_ellipse-fitting.py @@ -22,7 +22,7 @@ # set some default paths PATH_OUTPUT = update_path('output', absolute=True) -PATH_OVARY = os.path.join(update_path('data_images', absolute=True), 'drosophila_ovary_slice') +PATH_OVARY = os.path.join(update_path('data-images', absolute=True), 'drosophila_ovary_slice') PATH_IMAGES = os.path.join(PATH_OVARY, 'image') PATH_SEGM = os.path.join(PATH_OVARY, 'segm') PATH_ANNOT = os.path.join(PATH_OVARY, 'annot_eggs') @@ -33,6 +33,9 @@ TABLE_FB_PROBA = [[0.01, 0.7, 0.95, 0.8], [0.99, 0.3, 0.05, 0.2]] MAX_FIGURE_SEIZE = 10 +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) class TestEllipseFitting(unittest.TestCase): diff --git a/tests/test_graph-cut.py b/tests/test_graph-cut.py index 883e9661..32cba022 100644 --- a/tests/test_graph-cut.py +++ b/tests/test_graph-cut.py @@ -24,6 +24,9 @@ # set the output put directory PATH_OUTPUT = update_path('output', absolute=True) +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) class TestGraphCut(unittest.TestCase): diff --git a/tests/test_labeling.py b/tests/test_labeling.py index c643f817..57264513 100644 --- a/tests/test_labeling.py +++ b/tests/test_labeling.py @@ -20,6 +20,9 @@ # set the output put directory PATH_OUTPUT = update_path('output', absolute=True) +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) class TestLabels(unittest.TestCase): diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py index c6fe96b5..adb9441d 100644 --- a/tests/test_pipelines.py +++ b/tests/test_pipelines.py @@ -30,6 +30,9 @@ DEFAULT_SEGM_PARAMS = {'nb_classes': 2, 'dict_features': {'color': ['mean']}} imsegm.descriptors.USE_CYTHON = False +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) def show_segm_results_2d(img, seg, path_dir, fig_name='temp-segm_.png'): diff --git a/tests/test_region-growing.py b/tests/test_region-growing.py index e23a6490..9326f998 100644 --- a/tests/test_region-growing.py +++ b/tests/test_region-growing.py @@ -26,7 +26,7 @@ transform_rays_model_sets_mean_cdf_mixture, compute_segm_prob_fg, region_growing_shape_slic_greedy, region_growing_shape_slic_graphcut) -PATH_OVARY = os.path.join(update_path('data_images', absolute=True), +PATH_OVARY = os.path.join(update_path('data-images', absolute=True), 'drosophila_ovary_slice') PATH_IMAGE = os.path.join(PATH_OVARY, 'image') PATH_SEGM = os.path.join(PATH_OVARY, 'segm') @@ -38,6 +38,9 @@ LABELS_FG_PROB = (0.05, 0.7, 0.9, 0.9) DEFAULT_RG2SP_THRESHOLDS = RG2SP_THRESHOLDS FIG_SIZE = 12. +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) def compute_prior_map(cdist, size=(500, 800), step=5): diff --git a/tests/test_superpixels.py b/tests/test_superpixels.py index 6e2da5f3..bc9eed62 100644 --- a/tests/test_superpixels.py +++ b/tests/test_superpixels.py @@ -22,6 +22,9 @@ # set default output path PATH_OUTPUT = update_path('output', absolute=True) +# create output folder if needed +if not os.path.isdir(PATH_OUTPUT): + os.mkdir(PATH_OUTPUT) class TestSuperpixels(unittest.TestCase):