From ccc77cf95ffe3e65c4a8395e44f8f9ddad016d4f Mon Sep 17 00:00:00 2001 From: Gijs Date: Thu, 12 May 2022 10:51:51 +0200 Subject: [PATCH 1/4] Working on the readme --- README.md | 90 ++++++++++--------------------------------------------- 1 file changed, 15 insertions(+), 75 deletions(-) diff --git a/README.md b/README.md index 88d2f0d..f8a66b7 100644 --- a/README.md +++ b/README.md @@ -1,92 +1,32 @@ # Random_forest -Exploring random forest algorithm during residency Meise +Exploring random forest algorithm during residency Meise. -## Getting started +In this repository experiments with the random forest algorithm: a commented implementation to develop an understanding of its workings and a visualizer of the generated models. -To make it easy for you to get started with GitLab, here's a list of recommended next steps. -Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)! +## Files -## Add your files +The repository has an annotated version of the algorithm, a dataset with trainingdata and a visualizer. -- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files -- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command: +*commenting_code_model/random_forest_model_altered.py* an implementation of the Random Forest model. Commented during [Anaïs Bercks' residency in Meise](https://algoliterarypublishing.net/activities.html), and slighty altered to store the generated model into a json file. -``` -cd existing_repo -git remote add origin https://gitlab.constantvzw.org/anais_berck/random_forest.git -git branch -M main -git push -uf origin main -``` - -## Integrate with your tools - -- [ ] [Set up project integrations](https://gitlab.constantvzw.org/anais_berck/random_forest/-/settings/integrations) - -## Collaborate with your team - -- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/) -- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html) -- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically) -- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/) -- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html) - -## Test and Deploy - -Use the built-in continuous integration in GitLab. - -- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html) -- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/) -- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html) -- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/) -- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html) - -*** +*commenting_code_model/iris_data.csv* data set on Iris petals -# Editing this README +*commenting_code_model/visualizer/visualizer.py* the script visualizing a model generated by the *random_forest_model_altered.py* script. -When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template. +## Running -## Suggestions for a good README -Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information. -## Name -Choose a self-explaining name for your project. -## Description -Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. +## Requirements -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. +The implementations are written in python and require python 3, find information on how to [install python here](https://www.python.org/downloads/) -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. +The visualizer uses graphviz to generate the visualization. Find information on how to [install graphviz here](https://graphviz.org/download/) -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. +The visualizer also requires the [graphviz python bindings](https://pypi.org/project/graphviz). The easiest way to install them is through pip: -## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. - -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. - -## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. - -## Contributing -State if you are open to contributions and what your requirements are for accepting them. - -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. - -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. - -## Authors and acknowledgment -Show your appreciation to those who have contributed to the project. - -## License -For open source projects, say how it is licensed. - -## Project status -If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. +``` +pip3 install graphviz +``` \ No newline at end of file From 44222e5a13ffa3c6979c6365a0f6b60a179202c0 Mon Sep 17 00:00:00 2001 From: Gijs Date: Thu, 12 May 2022 11:24:01 +0200 Subject: [PATCH 2/4] Updated readme. Altered scripts to use absolute paths so they can be ran from everywhere and still place exports, or load imports from relative paths. --- .gitignore | 2 ++ README.md | 2 ++ .../random_forest_model_altered.py | 32 ++++++++++++------- .../visualizer/visualizer.py | 32 +++++++++++++++---- 4 files changed, 50 insertions(+), 18 deletions(-) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..976ba81 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*.pyc +commenting_code_model/visualizer/random_forest_model_tree_* diff --git a/README.md b/README.md index f8a66b7..592c8ee 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,9 @@ The repository has an annotated version of the algorithm, a dataset with trainin ## Running +Run the script *commenting_code_model/random_forest_model_altered.py* to generate random forests. The generated models will be json files in the same directory as the model. +Optionally run the *commenting_code_model/visualizer/visualizer.py* to generate visualizations. Those visualizations will the placed in the visualizer folder. ## Requirements diff --git a/commenting_code_model/random_forest_model_altered.py b/commenting_code_model/random_forest_model_altered.py index 015b54e..4b61e04 100644 --- a/commenting_code_model/random_forest_model_altered.py +++ b/commenting_code_model/random_forest_model_altered.py @@ -7,7 +7,12 @@ from random import randrange from csv import reader from math import sqrt import json - +import os.path + +# Get the directory of the current script to use in importing data +# and exporting the model. +basepath = os.path.dirname(os.path.realpath(__file__)) + # Load a CSV file. Definition of the function to read the csv and create dataset here def load_csv(filename): dataset = list() @@ -290,16 +295,17 @@ def bagging_predict(trees, row): return max(set(predictions), key=predictions.count) # Random Forest Algorithm -def random_forest(train, test, max_depth, min_size, sample_size, n_trees, n_features): +def random_forest(train, test, max_depth, min_size, sample_size, n_trees, n_features, model_path=None): trees = list() - for i in range(n_trees): + for _ in range(n_trees): sample = subsample(train, sample_size) # building a tree / root is dictionary with index, value, left/right) tree = build_tree(sample, max_depth, min_size, n_features) trees.append(tree) - with open('random_forest_model.json', 'w') as outfile: - json.dump(trees, outfile, indent = 6) + if model_path: + with open(model_path, 'w') as outfile: + json.dump(trees, outfile, indent = 6) # prediction using one of the folds we separated in the beginning, forest votes on every row of test data predictions = [bagging_predict(trees, row) for row in test] # returns votes/predictions of the forest @@ -311,7 +317,7 @@ def random_forest(train, test, max_depth, min_size, sample_size, n_trees, n_feat seed(2) # load and prepare data # filename = 'sonar_csv.csv' -filename = 'iris_data.csv' +filename = os.path.join(basepath, 'iris_data.csv') dataset = load_csv(filename) #print(dataset) # convert string attributes to integers @@ -331,8 +337,10 @@ sample_size = 1.0 # it specifies the size of the subset of features for the folds, where the size is close to the square root of the total number of features n_features = int(sqrt(len(dataset[0])-1)) # it tries forest of 1 tree, 5 trees, 10 trees + for n_trees in [1, 5, 10]: - scores = evaluate_algorithm(dataset, random_forest, n_folds, max_depth, min_size, sample_size, n_trees, n_features) + model_path = os.path.join(basepath, 'random_forest_model_{}-trees.json'.format(n_trees)) + scores = evaluate_algorithm(dataset, random_forest, n_folds, max_depth, min_size, sample_size, n_trees, n_features, model_path) print('Trees: %d' % n_trees) print('Scores: %s' % scores) print('Mean Accuracy: %.3f%%' % (sum(scores)/float(len(scores)))) @@ -344,8 +352,8 @@ for n_trees in [1, 5, 10]: #### pickle trees #### use: unpickle trees + bagging_predict with new data -with open('random_forest_model.json', 'r') as infile: - trees = json.load(infile) - prediction = bagging_predict(trees, dataset[23]) - # this gives a number, you have to reorganise model to get back the string of the class - print(prediction) \ No newline at end of file +# with open('random_forest_model.json', 'r') as infile: +# trees = json.load(infile) +# prediction = bagging_predict(trees, dataset[23]) +# # this gives a number, you have to reorganise model to get back the string of the class +# print(prediction) \ No newline at end of file diff --git a/commenting_code_model/visualizer/visualizer.py b/commenting_code_model/visualizer/visualizer.py index f1fe10a..f8cd3c3 100644 --- a/commenting_code_model/visualizer/visualizer.py +++ b/commenting_code_model/visualizer/visualizer.py @@ -59,16 +59,36 @@ def make_graph (graphname): graph.attr('graph', splines='line', rankdir='BT') return graph -def visualize (tree, graphname, generate_node_name = make_name_generator(length=3)): +def visualize (tree, graphname, generate_node_name = make_name_generator(length=3), directory=None): graph = make_graph(graphname) visualize_node(graph, generate_node_name, tree) - graph.render(graphname) + graph.render(graphname, directory=directory) if __name__ == '__main__': import json + import os.path + import glob + basepath = os.path.dirname(os.path.realpath(__file__)) + globpath = os.path.realpath(os.path.join(basepath, '..', 'random_forest_model_*-trees.json')) + + models = glob.glob(globpath) + + # Search for exported models + for modelpath in models: + print("Found {}".format(modelpath)) - with open('../random_forest_model.json', 'r') as file_in: - forest = json.load(file_in) + # Open model + with open(modelpath, 'r') as file_in: + # Parse the forest + forest = json.load(file_in) + modelname, _ = os.path.splitext(os.path.basename(modelpath)) + graphnamepattern = '{}_tree_{{}}'.format(modelname) - for idx, tree in enumerate(forest): - visualize(tree, 'random-tree-{}'.format(idx)) \ No newline at end of file + # Walk through the forest and visualize the trees + for idx, tree in enumerate(forest): + graphname = graphnamepattern.format(idx, len(forest)) + print('Visualizing tree {} of {}'.format(idx, len(forest))) + visualize(tree, graphname, directory=basepath) + print() + + print('Graphs placed in: {}'.format(basepath)) \ No newline at end of file From 09c379f48d4af5bdd7c72785cd04e320f9be3242 Mon Sep 17 00:00:00 2001 From: Gijs Date: Thu, 12 May 2022 11:27:50 +0200 Subject: [PATCH 3/4] Updated gitignore --- .gitignore | 4 +++- commenting_code_model/visualizer/requirements.txt | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) delete mode 100644 commenting_code_model/visualizer/requirements.txt diff --git a/.gitignore b/.gitignore index 976ba81..2155dda 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,4 @@ *.pyc -commenting_code_model/visualizer/random_forest_model_tree_* +commenting_code_model/visualizer/random_forest_model_* +commenting_code_model/random_forest_model_* +__pycache__ diff --git a/commenting_code_model/visualizer/requirements.txt b/commenting_code_model/visualizer/requirements.txt deleted file mode 100644 index abecf5d..0000000 --- a/commenting_code_model/visualizer/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -graphviz \ No newline at end of file From a8dac2ad230044fd492bdcaf0e4d855c453ac414 Mon Sep 17 00:00:00 2001 From: Gijs Date: Thu, 12 May 2022 11:30:35 +0200 Subject: [PATCH 4/4] Mentioned source of implentation in the readme. --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 592c8ee..6702c92 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ Exploring random forest algorithm during residency Meise. In this repository experiments with the random forest algorithm: a commented implementation to develop an understanding of its workings and a visualizer of the generated models. +The implementation was taken from [Machine Learning Mastery](https://machinelearningmastery.com/implement-random-forest-scratch-python/) + ## Files