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2f18860
Merge pull request #1 from NeuroNetMem/dev
davidespalla May 9, 2023
04af73c
Changed README
dabadav Jun 12, 2023
e405a92
Update README.md
dabadav Jun 12, 2023
013ff48
Update README.md
dabadav Jun 12, 2023
18bfcec
Changed README
dabadav Jun 12, 2023
be022ba
Changed README
dabadav Jun 12, 2023
ba02203
Changed README
dabadav Jun 12, 2023
ade74bb
Organized code, Docs, Poetry
dabadav Jun 13, 2023
07c8b4b
Changed README
dabadav Jun 13, 2023
f6cfa9b
Changed README
dabadav Jun 13, 2023
0099f0b
Changed README
dabadav Jun 13, 2023
098a66a
Changed README
dabadav Jun 13, 2023
9807e6a
Changed README
dabadav Jun 13, 2023
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Changed README
dabadav Jun 13, 2023
c5df207
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dabadav Jun 13, 2023
3395dbc
Changed README
dabadav Jun 13, 2023
570073b
Fix Dependencies poetry
dabadav Jun 13, 2023
9171d6e
Fix Dependencies poetry
dabadav Jun 13, 2023
37733fd
Fix Dependencies poetry
dabadav Jun 13, 2023
1b85e02
Fix Dependencies poetry
dabadav Jun 13, 2023
847a125
Fix Dependencies poetry
dabadav Jun 13, 2023
a4b45e2
Fix Dependencies poetry
dabadav Jun 13, 2023
925e814
Fix Dependencies poetry
dabadav Jun 13, 2023
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Fix Dependencies poetry
dabadav Jun 13, 2023
8d05d31
Fix Dependencies poetry
dabadav Jun 13, 2023
d518144
Fix Dependencies poetry
dabadav Jun 13, 2023
2968899
Fix Dependencies poetry
dabadav Jun 13, 2023
c38ac11
Fix Data Handling Class
dabadav Jun 13, 2023
adb4984
Fix Data Handling Class
dabadav Jun 13, 2023
b7d13a9
Fix Data Handling Class
dabadav Jun 13, 2023
da8edb2
Fix Data Handling Class
dabadav Jun 13, 2023
5fc296b
Fix Data Handling Class
dabadav Jun 13, 2023
7c16e28
Publish Docs
dabadav Jun 13, 2023
246adb3
Publish Docs
dabadav Jun 13, 2023
3757aa6
Publish Docs
dabadav Jun 13, 2023
3bc74e8
More Docs
dabadav Jun 13, 2023
0dc9bc3
More Docs
dabadav Jun 14, 2023
24a8577
More Docs
dabadav Jun 14, 2023
4d4bfa8
More Docs
dabadav Jun 14, 2023
78e6300
Restructure modules
dabadav Jun 15, 2023
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More Docs
dabadav Jun 15, 2023
fc95df0
More Docs
dabadav Jun 16, 2023
6597c69
Visualization functions
dabadav Jun 16, 2023
72fe3b4
New apply_mask function in vsdi.utils
Jun 16, 2023
b01881d
New VAE function to extract referecence latent dim image
Jun 18, 2023
4358cc8
Changed config
dabadav Jun 22, 2023
c250b51
Changed doc config
dabadav Jun 22, 2023
669e039
Changed doc config
dabadav Jun 22, 2023
6514c91
Changed config, added dependencies
dabadav Jun 22, 2023
7c1a3eb
Changed config, added dependencies
dabadav Jun 22, 2023
cc613e2
Changed config, added dependencies
dabadav Jun 22, 2023
7231fdf
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dabadav Jun 22, 2023
58b84ff
Changed config, added dependencies
dabadav Jun 22, 2023
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Changed config, added dependencies
dabadav Jun 22, 2023
a65abd7
Changed config, added dependencies
dabadav Jun 22, 2023
d7e4102
Changed config, added dependencies
dabadav Jun 22, 2023
899ce38
Changed config, added dependencies
dabadav Jun 22, 2023
d1e3dd1
Changed config, added dependencies
dabadav Jun 22, 2023
2662b21
Changed config, added dependencies
dabadav Jun 22, 2023
f4d10f4
Changed config, added dependencies
dabadav Jun 22, 2023
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Changed config, added dependencies
dabadav Jun 22, 2023
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Changed config, added dependencies
dabadav Jun 22, 2023
e729acd
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dabadav Jun 22, 2023
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dabadav Jun 22, 2023
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dabadav Jun 22, 2023
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32 changes: 32 additions & 0 deletions .readthedocs.yaml
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# Read the Docs configuration file for Sphinx projects
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the OS, Python version and other tools you might need
build:
os: ubuntu-22.04
tools:
python: "3.11"
# nodejs: "19"
# rust: "1.64"
# golang: "1.19"

# Build documentation in the "docs/" directory with Sphinx
sphinx:
configuration: docs/source/conf.py

# Optionally build your docs in additional formats such as PDF and ePub
# formats:
# - pdf
# - epub

# Optional but recommended, declare the Python requirements required
# to build your documentation
# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
python:
install:
- method: pip
path: .
- requirements: docs/source/requirements.txt
56 changes: 52 additions & 4 deletions README.md
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# pipeline_vsdi
<h1 align="center">
<img src="https://images.squarespace-cdn.com/content/v1/6172d4d5e7f28f6b50179b1b/c3b7cc24-51a1-44aa-8b39-b5e94ac01e8d/image+%282%29.png">
<br>Pipeline VSDI
</h1><br>

Preprocessing tools for voltage sensitive dye imaging data

## Structure

- vsdi will contain classes for handling sessions and full datasets
- preprocessing contains functionality to clean and reshape data
- dim_reduction contains functionality to reduce the dimensionality of the data with different models
- **vsdi** - Contains classes for handling sessions and full datasets.
- **preprocessing** - Contains functionality to clean and reshape data.
- **dim_reduction** - Contains functionality to reduce the dimensionality of the data with different models.

## Installation

### Prerequisites

- Python 3.7 or higher
- [Poetry](https://python-poetry.org/docs/#installation) Python packaging and dependency management tool.

### Steps

#### 1. Clone the repository

```bash
git clone https://github.com/dabadav/pipeline_vsdi.git
cd pipeline_vsdi
```

#### 2. Install the package using Poetry

Ensure you're in the `pipeline_vsdi` directory (or the directory where you cloned your repository) and run:

```bash
poetry install
```

This command installs all the dependencies specified in the `pyproject.toml` file in a new virtual environment. If you want to use the virtual environment for other tasks, you can activate it using:

```bash
poetry shell
```

After this, you should have all the necessary dependencies installed and be able to use the functionality provided by the Pipeline VSDI.

## Usage

After installation, you can import and use the tools in the Python interpreter or your scripts like:

```python
from vsdi import Session
from preprocessing import clean_data
from dim_reduction import reduce_dimension

# Use the tools as per your requirement.
```
46 changes: 0 additions & 46 deletions dim_reduction/clustering.py

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358 changes: 0 additions & 358 deletions dim_reduction/pca_ica.ipynb

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166 changes: 0 additions & 166 deletions dim_reduction/pipeline.py

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