Improve analysis

[lauraporta]

@openai: ignore ☝🏻stops future reviews of the bot

👉🏻 @ Future human reviewer

I am experimenting using a chatgpt bot to have PR reviewed, while waiting for copilot X to arrive.

The bot is not able to process files that are too large, and unfortunately those are the core of the PR. These files are:

• spatial_freq_temporal_freq.py
• photon_data.py

So no summary and no comments on the code are provided for these two files. Therefore I have updated the descriptions of the bot filling them up with the missing info.

I noticed also that applies comments relevant to one file in the wrong file. I'll see if I can move them around. Sorry about that.

⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️ N.B.: a previous PR (#25) had many relevant suggestions that are still applicable to this one. They are not addressed in this PR since they require extensive refactoring. This PR is mostly focused on adding new functionalities and writing better tests. ⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️⚠️

Finally, these changes where actually done while developing the dashboard, which you can find in the commits. Please ignore any changes related to it. I have split the changes related to the analysis and put them all in this PR to keep things cleaner.

Laura's summary

Broad description of the main changes:

• The application can now be asily started by running python3 demo_cly.py in your environment. app.py substitutes what main.py was and now allows us to save the analysis result as an object to be then used by the dashboard.
• The analysis class is now called FrequencyResponsiveness and used with the name responsiveness for short when instantiated.
• Anything that can be considered "data", analysed or not, is stored in responsiveness.data which is a PhotonData object. Anything else in responsiveness is a method that takes care of one bit of the analysis. On instantiation, FrequencyResponsiveness has the attribute data evaluated.
• PhotonData has been changed to accomodate this changes. Now all the attributes that will be filled by the analysis are instantiated at the creation of the PhotonData object. Now in the docstring of the class there is a list of all possible attributes. I added some checks to evaluate the internal consistency of the datasets with expected resutls.
• the analysis pipeline is now triggered with __call__, by simply calling the instantiated object: responsiveness(). The analysis pipeline consists of:
  1. calculating statistics (not changed)
  2. fitting the response to a gaussian and storing the values in data. The methods dealing with this part are what has been added to the class.
• The methods in the part 2 of the analysis call methods contained in gaussian_calculations.py. They are static methods describing the gaussian equation in use and the way to fit the data to it.
• Tests have been improved by adding a script to generate expected outputs in order to be compared with the tests results. The results are stored in a folder called mock_data/. This new feature required changes in the tests, in conftest.py and the creation of a shared set of helper methods in generate_mock_data.py.
• I am starting to document the comparisons that I have made with my code and the original matlab codebase in the docs.
• There are overall various refactorying changes and a more widespread use of typing. Some docstrings have been improved.

Summary by OpenAI

Release Notes:

• New Feature: Added fitting parameters to the config file and modified some existing parameters such as fps_tree_photon, spatial_frequencies, temporal_frequencies, directions, n_spatial_frequencies, and n_temporal_frequencies.
• Refactor: Improved the structure of the application by replacing the main function with a new app.py file that allows the application to be started by running python3 demo_cly.py.
• Documentation: Improved the documentation of classes and their methods. It adds more details to the docstrings, clarifies some comments, and fixes typos.
• Test: Added unit tests for Gaussian-related methods in gaussians_calculations.py.

Changes abound, code quality improved, Bugs squashed, docs clarified, tests approved, With new features added, and refactorings too, This PR brings joy, and we thank you! 🎉👏

[github-actions[bot]]

:robot: OpenAI

High-level Summary

The changes made to the codebase include improvements in logic, security, performance, data races, consistency, error handling, maintainability, modularity, complexity, and optimization. The changeset includes modifications to various files such as .gitignore, MANIFEST.in, demo_cli.py, app.py, config_switches.py, load_data.py, data_raw.py, parser2p.py, parser2pRSP.py, and test files. The changes involve adding new parameters to the config file, refactoring functions, improving documentation, adding unit tests, and modifying the application's structure to improve its usability.

Files Summary

File	Changes
.gitignore, setup_for_demo.py	Added .pickle and .obsidian to .gitignore file. Added fitting parameters to the config file and modified some existing parameters such as fps_tree_photon, spatial_frequencies, temporal_frequencies, directions, n_spatial_frequencies, n_temporal_frequencies, and n_directions.
MANIFEST.in	Added two lines to include documentation files in the distribution package. Removed a line that includes YAML files and does not exclude .md and .png files from being included.
demo_cli.py, rsp_vision/main.py	Added import statement and calls analysis_pipeline() function if it exists. The main function has been removed and replaced with a new app.py file that allows the application to be started by running python3 demo_cly.py. The analysis class is now called FrequencyResponsiveness and used with the name responsiveness for short when instantiated. The PhotonData object has been changed to accommodate these changes.
docs/reproduce_matlab_output.md	Added proof of accurate MATLAB output reproduction and comparison with Python implementation. Handles NaN values better in the new implementation.
rsp_vision/console_application/app.py	Added a decorator to handle exceptions, a function to start logging, and a function to get the name of the module for logging purposes. The main function now uses rich.prompt to get input from the user instead of command-line arguments. Imported new modules and classes, such as logging, pickle, rich, and PhotonData.
rsp_vision/load/config_switches.py, rsp_vision/load/load_data.py	Refactored get_fps function to include type hints and remove unused ascii_array_to_string function. The read function is removed and replaced with read_config_file. The yaml module is imported. The load_data function now calls a new function load_data_from_filename which replaces the old load function. A new function read_config_file is added to read the configuration file.
rsp_vision/objects/data_raw.py, rsp_vision/objects/file.py, rsp_vision/objects/folder_naming_specs.py	Improved the documentation of classes and their methods. It adds more details to the docstrings, clarifies some comments, and fixes typos.
rsp_vision/objects/parsers2p/parser2p.py, rsp_vision/objects/parsers2p/parser2pRSP.py	The changes in parser2p.py involve minor modifications to the docstrings and comments. The changes improve readability and do not introduce new functionality or modify existing logic. The diff updates the docstrings and formatting of Parser2pRSP class in parser2pRSP.py. It also updates the comments and formatting of some methods.
tests/test_integration/calculate_outputs.py, tests/test_integration/generate_mock_data.py, tests/test_integration/test_photon_data.py, tests/test_integration/test_sf_tf.py, tests/test_integration/test_photon_data.py, tests/test_integration/test_sf_tf_static_methods.py	Minor changes to add fixtures, rename variables, and use fixtures instead of functions for testing purposes. No issues with logic, security, performance, data races, consistency, error handling, maintainability, modularity, complexity, or optimization were found.
tests/test_unit/test_gaussian_related_methods.py	Added unit tests for Gaussian-related methods in gaussians_calculations.py. Tests include functions to fit a 2D Gaussian to data, create a Gaussian matrix, and perform a single Gaussian fit.

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Files ignored due to filter (1)

### Ignored files * tox.ini

Files not summarized due to errors (5)

### Failed to summarize * rsp_vision/analysis/gaussians_calculations.py (diff tokens exceeds limit) * rsp_vision/analysis/spatial_freq_temporal_freq.py (diff tokens exceeds limit) * rsp_vision/objects/photon_data.py (diff tokens exceeds limit) * tests/test_integration/generate_mock_data.py (diff tokens exceeds limit) * tests/test_integration/test_sf_tf.py (diff tokens exceeds limit)

Files not reviewed due to simple changes (23)

### Skipped review * .gitignore * MANIFEST.in * demo_cli.py * docs/reproduce_matlab_output.md * rsp_vision/console_application/app.py * rsp_vision/load/config_switches.py * rsp_vision/load/load_data.py * rsp_vision/load/read_config.py * rsp_vision/main.py * rsp_vision/objects/data_raw.py * rsp_vision/objects/file.py * rsp_vision/objects/folder_naming_specs.py * rsp_vision/objects/parsers2p/parser2p.py * rsp_vision/objects/parsers2p/parser2pRSP.py * rsp_vision/plots/plotter.py * rsp_vision/utils.py * setup_for_demo.py * tests/conftest.py * tests/test_integration/calculate_outputs.py * tests/test_integration/test_photon_data.py * tests/test_integration/test_sf_tf_static_methods.py * tests/test_unit/test_gaussian_related_methods.py * tests/test_unit/test_utils.py

[lauraporta]

Joe, thanks for all your comments and suggestions. Right now I would not address them, I add them to the backlog of the possible improvements that I could do in the future.