erge branch 'main' of https://gitlab.constantvzw.org/anais_berck/random_forest

.gitignore

@@ -0,0 +1,4 @@
+*.pyc
+commenting_code_model/visualizer/random_forest_model_*
+commenting_code_model/random_forest_model_*
+__pycache__

README.md

@@ -1,92 +1,36 @@
 # 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.
+The implementation was taken from [Machine Learning Mastery](https://machinelearningmastery.com/implement-random-forest-scratch-python/)
 
-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)!
 
-## Add your files
+## Files
 
-- [ ] [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
+The repository has an annotated version of the algorithm, a dataset with trainingdata and a visualizer.
-- [ ] [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)
-
-***
 
-# Editing this README
+*commenting_code_model/iris_data.csv* data set on Iris petals
 
-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.
+*commenting_code_model/visualizer/visualizer.py* the script visualizing a model generated by the *random_forest_model_altered.py* script.
 
-## Suggestions for a good README
+## Running
-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
+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.
-Choose a self-explaining name for your project.
 
-## Description
+Optionally run the *commenting_code_model/visualizer/visualizer.py* to generate visualizations. Those visualizations will the placed in the visualizer folder.
-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.
 
-## Badges
+## Requirements
-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.
 
-## Visuals
+The implementations are written in python and require python 3, find information on how to [install python here](https://www.python.org/downloads/)
-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.
 
-## Installation
+The visualizer uses graphviz to generate the visualization. Find information on how to [install graphviz here](https://graphviz.org/download/)
-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.
 
-## Usage
+The visualizer also requires the [graphviz python bindings](https://pypi.org/project/graphviz). The easiest way to install them is through pip:
-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.
+pip3 install graphviz
-
+```
-## 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.

commenting_code_model/random_forest_model_altered.py

@@ -7,6 +7,11 @@ 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):
@@ -290,15 +295,16 @@ 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:
+	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]
@@ -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:
+# with open('random_forest_model.json', 'r') as infile:
-	trees = json.load(infile)
+# 	trees = json.load(infile)
-	prediction = bagging_predict(trees, dataset[23])
+# 	prediction = bagging_predict(trees, dataset[23])
-	# this gives a number, you have to reorganise model to get back the string of the class
+# 	# this gives a number, you have to reorganise model to get back the string of the class
-	print(prediction)
+# 	print(prediction)

commenting_code_model/visualizer/requirements.txt

@@ -1 +0,0 @@
-graphviz

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'))
   
-  with open('../random_forest_model.json', 'r') as file_in:
+  models = glob.glob(globpath)
+
+  # Search for exported models
+  for modelpath in models:
+    print("Found {}".format(modelpath))
+
+    # 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)
 
+      # Walk through the forest and visualize the trees
       for idx, tree in enumerate(forest):
-      visualize(tree, 'random-tree-{}'.format(idx))
+        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))