From b85ee9d64a536937912544c7bbd5b98b635b7e8d Mon Sep 17 00:00:00 2001
From: Christian C <cc@localhost>
Date: Mon, 11 Nov 2024 12:29:32 -0800
Subject: Initial commit

---
 code/sunlab/common/__init__.py                     |   5 +
 code/sunlab/common/data/__init__.py                |   6 +
 code/sunlab/common/data/basic.py                   |   6 +
 code/sunlab/common/data/dataset.py                 | 255 +++++++++++++++++++
 code/sunlab/common/data/dataset_iterator.py        |  34 +++
 code/sunlab/common/data/image_dataset.py           |  75 ++++++
 code/sunlab/common/data/shape_dataset.py           |  57 +++++
 code/sunlab/common/data/utilities.py               | 119 +++++++++
 code/sunlab/common/distribution/__init__.py        |   7 +
 .../distribution/adversarial_distribution.py       |  35 +++
 .../common/distribution/gaussian_distribution.py   |  23 ++
 .../common/distribution/o_gaussian_distribution.py |  38 +++
 .../common/distribution/s_gaussian_distribution.py |  40 +++
 .../common/distribution/swiss_roll_distribution.py |  42 ++++
 .../distribution/symmetric_uniform_distribution.py |  21 ++
 .../common/distribution/uniform_distribution.py    |  21 ++
 .../common/distribution/x_gaussian_distribution.py |  38 +++
 code/sunlab/common/mathlib/__init__.py             |   1 +
 code/sunlab/common/mathlib/base.py                 |  57 +++++
 code/sunlab/common/mathlib/lyapunov.py             |  54 +++++
 code/sunlab/common/mathlib/random_walks.py         |  83 +++++++
 code/sunlab/common/plotting/__init__.py            |   2 +
 code/sunlab/common/plotting/base.py                | 270 +++++++++++++++++++++
 code/sunlab/common/plotting/colors.py              |  38 +++
 code/sunlab/common/scaler/__init__.py              |   2 +
 code/sunlab/common/scaler/adversarial_scaler.py    |  44 ++++
 code/sunlab/common/scaler/max_abs_scaler.py        |  48 ++++
 code/sunlab/common/scaler/quantile_scaler.py       |  52 ++++
 28 files changed, 1473 insertions(+)
 create mode 100644 code/sunlab/common/__init__.py
 create mode 100644 code/sunlab/common/data/__init__.py
 create mode 100644 code/sunlab/common/data/basic.py
 create mode 100644 code/sunlab/common/data/dataset.py
 create mode 100644 code/sunlab/common/data/dataset_iterator.py
 create mode 100644 code/sunlab/common/data/image_dataset.py
 create mode 100644 code/sunlab/common/data/shape_dataset.py
 create mode 100644 code/sunlab/common/data/utilities.py
 create mode 100644 code/sunlab/common/distribution/__init__.py
 create mode 100644 code/sunlab/common/distribution/adversarial_distribution.py
 create mode 100644 code/sunlab/common/distribution/gaussian_distribution.py
 create mode 100644 code/sunlab/common/distribution/o_gaussian_distribution.py
 create mode 100644 code/sunlab/common/distribution/s_gaussian_distribution.py
 create mode 100644 code/sunlab/common/distribution/swiss_roll_distribution.py
 create mode 100644 code/sunlab/common/distribution/symmetric_uniform_distribution.py
 create mode 100644 code/sunlab/common/distribution/uniform_distribution.py
 create mode 100644 code/sunlab/common/distribution/x_gaussian_distribution.py
 create mode 100644 code/sunlab/common/mathlib/__init__.py
 create mode 100644 code/sunlab/common/mathlib/base.py
 create mode 100644 code/sunlab/common/mathlib/lyapunov.py
 create mode 100644 code/sunlab/common/mathlib/random_walks.py
 create mode 100644 code/sunlab/common/plotting/__init__.py
 create mode 100644 code/sunlab/common/plotting/base.py
 create mode 100644 code/sunlab/common/plotting/colors.py
 create mode 100644 code/sunlab/common/scaler/__init__.py
 create mode 100644 code/sunlab/common/scaler/adversarial_scaler.py
 create mode 100644 code/sunlab/common/scaler/max_abs_scaler.py
 create mode 100644 code/sunlab/common/scaler/quantile_scaler.py

(limited to 'code/sunlab/common')

diff --git a/code/sunlab/common/__init__.py b/code/sunlab/common/__init__.py
new file mode 100644
index 0000000..cb6716c
--- /dev/null
+++ b/code/sunlab/common/__init__.py
@@ -0,0 +1,5 @@
+from .data import *
+from .distribution import *
+from .scaler import *
+from .mathlib import *
+from .plotting import *
diff --git a/code/sunlab/common/data/__init__.py b/code/sunlab/common/data/__init__.py
new file mode 100644
index 0000000..3e26874
--- /dev/null
+++ b/code/sunlab/common/data/__init__.py
@@ -0,0 +1,6 @@
+from .basic import *
+from .dataset import *
+from .dataset_iterator import *
+from .shape_dataset import *
+from .image_dataset import *
+from .utilities import *
diff --git a/code/sunlab/common/data/basic.py b/code/sunlab/common/data/basic.py
new file mode 100644
index 0000000..bb2e912
--- /dev/null
+++ b/code/sunlab/common/data/basic.py
@@ -0,0 +1,6 @@
+import numpy
+
+
+numpy.load_dat = lambda *args, **kwargs: numpy.load(
+    *args, **kwargs, allow_pickle=True
+).item()
diff --git a/code/sunlab/common/data/dataset.py b/code/sunlab/common/data/dataset.py
new file mode 100644
index 0000000..8589abf
--- /dev/null
+++ b/code/sunlab/common/data/dataset.py
@@ -0,0 +1,255 @@
+from .dataset_iterator import DatasetIterator
+
+
+class Dataset:
+    """# Dataset Superclass"""
+
+    base_scale = 10.0
+
+    def __init__(
+        self,
+        dataset_filename,
+        data_columns=[],
+        label_columns=[],
+        batch_size=None,
+        shuffle=False,
+        val_split=0.0,
+        scaler=None,
+        sort_columns=None,
+        random_seed=4332,
+        pre_scale=10.0,
+        **kwargs
+    ):
+        """# Initialize Dataset
+        self.dataset = dataset (N, ...)
+        self.labels = labels (N, ...)
+
+        Optional Arguments:
+        - prescale_function: The function that takes the ratio and transforms
+        the dataset by multiplying the prescale_function output
+        - sort_columns: The columns to sort the data by initially
+        - equal_split: If the classifications should be equally split in
+        training"""
+        from pandas import read_csv
+        from numpy import array, all
+        from numpy.random import seed
+
+        if seed is not None:
+            seed(random_seed)
+
+        # Basic Dataset Information
+        self.data_columns = data_columns
+        self.label_columns = label_columns
+        self.source = dataset_filename
+        self.dataframe = read_csv(self.source)
+
+        # Pre-scaling Transformation
+        prescale_ratio = self.base_scale / pre_scale
+        ratio = prescale_ratio
+        prescale_powers = array([2, 1, 1, 0, 2, 1, 0, 0, 1, 1, 1, 1, 1])
+        if "prescale_function" in kwargs.keys():
+            prescale_function = kwargs["prescale_function"]
+        else:
+
+            def prescale_function(x):
+                return x**prescale_powers
+
+        self.prescale_function = prescale_function
+        self.prescale_factor = self.prescale_function(ratio)
+        assert (
+            len(data_columns) == self.prescale_factor.shape[0]
+        ), "Column Mismatch on Prescale"
+        self.original_scale = pre_scale
+
+        # Scaling Transformation
+        self.scaled = scaler is not None
+        self.scaler = scaler
+
+        # Training Dataset Information
+        self.do_split = False if val_split == 0.0 else True
+        self.validation_split = val_split
+        self.batch_size = batch_size
+        self.do_shuffle = shuffle
+        self.equal_split = False
+        if "equal_split" in kwargs.keys():
+            self.equal_split = kwargs["equal_split"]
+
+        # Classification Labels if they exist
+        self.dataset = self.dataframe[self.data_columns].to_numpy()
+        if len(self.label_columns) == 0:
+            self.labels = None
+        elif not all([column in self.dataframe.columns for column in label_columns]):
+            import warnings
+
+            warnings.warn(
+                "No classification labels found for the dataset", RuntimeWarning
+            )
+            self.labels = None
+        else:
+            self.labels = self.dataframe[self.label_columns].squeeze()
+
+        # Initialize the dataset
+        if "sort_columns" in kwargs.keys():
+            self.sort(kwargs["sort_columns"])
+        if self.do_shuffle:
+            self.shuffle()
+        if self.do_split:
+            self.split()
+        self.refresh_dataset()
+
+    def __len__(self):
+        """# Get how many cases are in the dataset"""
+        return self.dataset.shape[0]
+
+    def __getitem__(self, idx):
+        """# Make Dataset Sliceable"""
+        idx_slice = None
+        slice_stride = 1 if self.batch_size is None else self.batch_size
+        # If we pass a slice, return the slice
+        if type(idx) == slice:
+            idx_slice = idx
+        # If we pass an int, return a batch-size slice
+        else:
+            idx_slice = slice(
+                idx * slice_stride, min([len(self), (idx + 1) * slice_stride])
+            )
+        if self.labels is None:
+            return self.dataset[idx_slice, ...]
+        return self.dataset[idx_slice, ...], self.labels[idx_slice, ...]
+
+    def scale_data(self, data):
+        """# Scale dataset from scaling function"""
+        data = data * self.prescale_factor
+        if not (self.scaler is None):
+            data = self.scaler(data)
+        return data
+
+    def scale(self):
+        """# Scale Dataset"""
+        self.dataset = self.scale_data(self.dataset)
+
+    def refresh_dataset(self, dataframe=None):
+        """# Refresh Dataset
+
+        Regenerate the dataset from a dataframe.
+        Primarily used after a sort or filter."""
+        if dataframe is None:
+            dataframe = self.dataframe
+        self.dataset = dataframe[self.data_columns].to_numpy()
+        if self.labels is not None:
+            self.labels = dataframe[self.label_columns].to_numpy().squeeze()
+        self.scale()
+
+    def sort_on(self, columns):
+        """# Sort Dataset on Column(s)"""
+        from numpy import all
+
+        if type(columns) == str:
+            columns = [columns]
+        if columns is not None:
+            assert all(
+                [column in self.dataframe.columns for column in columns]
+            ), "Dataframe does not contain some provided columns!"
+            self.dataframe = self.dataframe.sort_values(by=columns)
+            self.refresh_dataset()
+
+    def filter_on(self, column, value):
+        """# Filter Dataset on Column Value(s)"""
+        assert column in self.dataframe.columns, "Column DNE"
+        self.working_dataset = self.dataframe[self.dataframe[column].isin(value)]
+        self.refresh_dataset(self.working_dataset)
+
+    def filter_off(self):
+        """# Remove any filter on the dataset"""
+        self.refresh_dataset()
+
+    def unique(self, column):
+        """# Get unique values in a column(s)"""
+        assert column in self.dataframe.columns, "Column DNE"
+        from numpy import unique
+
+        return unique(self.dataframe[column])
+
+    def shuffle_data(self, data, labels=None):
+        """# Shuffle a dataset"""
+        from numpy.random import permutation
+
+        shuffled = permutation(data.shape[0])
+        if labels is not None:
+            assert (
+                self.labels.shape[0] == self.dataset.shape[0]
+            ), "Dataset and Label Shape Mismatch"
+            shuf_data = data[shuffled, ...]
+            shuf_labels = labels[shuffled]
+            if len(labels.shape) > 1:
+                shuf_labels = labels[shuffled,...]
+            return shuf_data, shuf_labels
+        return data[shuffled, ...]
+
+    def shuffle(self):
+        """# Shuffle the dataset"""
+        if self.do_shuffle:
+            if self.labels is None:
+                self.dataset = self.shuffle_data(self.dataset)
+            self.dataset, self.labels = self.shuffle_data(self.dataset, self.labels)
+
+    def split(self):
+        """# Training/ Validation Splitting"""
+        from numpy import floor, unique, where, hstack, delete
+        from numpy.random import permutation
+
+        equal_classes = self.equal_split
+        if not self.do_split:
+            return
+        assert self.validation_split <= 1.0, "Too High"
+        assert self.validation_split > 0.0, "Too Low"
+        train_count = int(floor(self.dataset.shape[0] * (1 - self.validation_split)))
+        training_data = self.dataset[:train_count, ...]
+        training_labels = None
+        validation_data = self.dataset[train_count:, ...]
+        validation_labels = None
+        if self.labels is not None:
+            if equal_classes:
+                # Ensure the split balances the prevalence of each class
+                assert len(self.labels.shape) == 1, "1D Classification Only Currently"
+                classification_breakdown = unique(self.labels, return_counts=True)
+                train_count = min(
+                    [
+                        train_count,
+                        classification_breakdown.shape[0]
+                        * min(classification_breakdown[1]),
+                    ]
+                )
+                class_size = train_count / classification_breakdown.shape[0]
+                class_indicies = [
+                    permutation(where(self.labels == _class)[0])
+                    for _class in classification_breakdown[0]
+                ]
+                class_indicies = [indexes[:class_size] for indexes in class_indicies]
+                train_class_indicies = hstack(class_indicies).squeeze()
+                train_class_indicies = permutation(train_class_indicies)
+                training_data = self.dataset[train_class_indicies, ...]
+                training_labels = self.labels[train_class_indicies]
+                if len(self.labels.shape) > 1:
+                    training_labels = self.labels[train_class_indicies,...]
+                validation_data = delete(self.dataset, train_class_indicies, axis=0)
+                validation_labels = delete(
+                    self.labels, train_class_indicies, axis=0
+                ).squeeze()
+            else:
+                training_labels = self.labels[:train_count]
+                if len(training_labels.shape) > 1:
+                    training_labels = self.labels[:train_count, ...]
+                validation_labels = self.labels[train_count:]
+                if len(validation_labels.shape) > 1:
+                    validation_labels = self.labels[train_count:, ...]
+        self.training_data = training_data
+        self.validation_data = validation_data
+        self.training = DatasetIterator(training_data, training_labels, self.batch_size)
+        self.validation = DatasetIterator(
+            validation_data, validation_labels, self.batch_size
+        )
+
+    def reset_iterators(self):
+        """# Reset Train/ Validation Iterators"""
+        self.split()
diff --git a/code/sunlab/common/data/dataset_iterator.py b/code/sunlab/common/data/dataset_iterator.py
new file mode 100644
index 0000000..7c91caa
--- /dev/null
+++ b/code/sunlab/common/data/dataset_iterator.py
@@ -0,0 +1,34 @@
+class DatasetIterator:
+    """# Dataset Iterator
+
+    Creates an iterator object on a dataset and labels"""
+
+    def __init__(self, dataset, labels=None, batch_size=None):
+        """# Initialize the iterator with the dataset and labels
+
+        - batch_size: How many to include in the iteration"""
+        self.dataset = dataset
+        self.labels = labels
+        self.current = 0
+        self.batch_size = (
+            batch_size if batch_size is not None else self.dataset.shape[0]
+        )
+
+    def __iter__(self):
+        """# Iterator Function"""
+        return self
+
+    def __next__(self):
+        """# Next Iteration
+
+        Slice the dataset and labels to provide"""
+        self.cur = self.current
+        self.current += 1
+        if self.cur * self.batch_size < self.dataset.shape[0]:
+            iterator_slice = slice(
+                self.cur * self.batch_size, (self.cur + 1) * self.batch_size
+            )
+            if self.labels is None:
+                return self.dataset[iterator_slice, ...]
+            return self.dataset[iterator_slice, ...], self.labels[iterator_slice, ...]
+        raise StopIteration
diff --git a/code/sunlab/common/data/image_dataset.py b/code/sunlab/common/data/image_dataset.py
new file mode 100644
index 0000000..46e77b6
--- /dev/null
+++ b/code/sunlab/common/data/image_dataset.py
@@ -0,0 +1,75 @@
+class ImageDataset:
+    def __init__(
+        self,
+        base_directory,
+        ext="png",
+        channels=[0],
+        batch_size=None,
+        shuffle=False,
+        rotate=False,
+        rotate_p=1.,
+    ):
+        """# Image Dataset
+
+        Load a directory of images"""
+        from glob import glob
+        from matplotlib.pyplot import imread
+        from numpy import newaxis, vstack
+        from numpy.random import permutation, rand
+
+        self.base_directory = base_directory
+        files = glob(self.base_directory + "*." + ext)
+        self.dataset = []
+        for file in files:
+            im = imread(file)[newaxis, :, :, channels].transpose(0, 3, 1, 2)
+            self.dataset.append(im)
+            # Also add rotations of the image to the dataset
+            if rotate:
+                if rand() < rotate_p:
+                    self.dataset.append(im[:, :, ::-1, :])
+                if rand() < rotate_p:
+                    self.dataset.append(im[:, :, :, ::-1])
+                if rand() < rotate_p:
+                    self.dataset.append(im[:, :, ::-1, ::-1])
+                if rand() < rotate_p:
+                    self.dataset.append(im.transpose(0, 1, 3, 2))
+                if rand() < rotate_p:
+                    self.dataset.append(im.transpose(0, 1, 3, 2)[:, :, ::-1, :])
+                if rand() < rotate_p:
+                    self.dataset.append(im.transpose(0, 1, 3, 2)[:, :, :, ::-1])
+                if rand() < rotate_p:
+                    self.dataset.append(im.transpose(0, 1, 3, 2)[:, :, ::-1, ::-1])
+        self.dataset = vstack(self.dataset)
+        if shuffle:
+            self.dataset = self.dataset[permutation(self.dataset.shape[0]), ...]
+        self.batch_size = (
+            batch_size if batch_size is not None else self.dataset.shape[0]
+        )
+
+    def torch(self, device=None):
+        """# Cast to Torch Tensor"""
+        import torch
+
+        if device is None:
+            device = torch.device("cpu")
+        return torch.tensor(self.dataset).to(device)
+
+    def numpy(self):
+        """# Cast to Numpy Array"""
+        return self.dataset
+
+    def __len__(self):
+        """# Return Number of Cases
+
+        (or Number in each Batch)"""
+        return self.dataset.shape[0] // self.batch_size
+
+    def __getitem__(self, index):
+        """# Slice By Batch"""
+        if type(index) == tuple:
+            return self.dataset[index]
+        elif type(index) == int:
+            return self.dataset[
+                index * self.batch_size : (index + 1) * self.batch_size, ...
+            ]
+        return
diff --git a/code/sunlab/common/data/shape_dataset.py b/code/sunlab/common/data/shape_dataset.py
new file mode 100644
index 0000000..5a68736
--- /dev/null
+++ b/code/sunlab/common/data/shape_dataset.py
@@ -0,0 +1,57 @@
+from .dataset import Dataset
+
+
+class ShapeDataset(Dataset):
+    """# Shape Dataset"""
+
+    def __init__(
+        self,
+        dataset_filename,
+        data_columns=[
+            "Area",
+            "MjrAxisLength",
+            "MnrAxisLength",
+            "Eccentricity",
+            "ConvexArea",
+            "EquivDiameter",
+            "Solidity",
+            "Extent",
+            "Perimeter",
+            "ConvexPerim",
+            "FibLen",
+            "InscribeR",
+            "BlebLen",
+        ],
+        label_columns=["Class"],
+        batch_size=None,
+        shuffle=False,
+        val_split=0.0,
+        scaler=None,
+        sort_columns=None,
+        random_seed=4332,
+        pre_scale=10,
+        **kwargs
+    ):
+        """# Initialize Dataset
+        self.dataset = dataset (N, ...)
+        self.labels = labels (N, ...)
+
+        Optional Arguments:
+        - prescale_function: The function that takes the ratio and transforms
+        the dataset by multiplying the prescale_function output
+        - sort_columns: The columns to sort the data by initially
+        - equal_split: If the classifications should be equally split in
+        training"""
+        super().__init__(
+            dataset_filename,
+            data_columns=data_columns,
+            label_columns=label_columns,
+            batch_size=batch_size,
+            shuffle=shuffle,
+            val_split=val_split,
+            scaler=scaler,
+            sort_columns=sort_columns,
+            random_seed=random_seed,
+            pre_scale=pre_scale,
+            **kwargs
+        )
diff --git a/code/sunlab/common/data/utilities.py b/code/sunlab/common/data/utilities.py
new file mode 100644
index 0000000..6b4e6f3
--- /dev/null
+++ b/code/sunlab/common/data/utilities.py
@@ -0,0 +1,119 @@
+from .shape_dataset import ShapeDataset
+from ..scaler.max_abs_scaler import MaxAbsScaler
+
+
+def import_10x(
+    filename,
+    magnification=10,
+    batch_size=None,
+    shuffle=False,
+    val_split=0.0,
+    scaler=None,
+    sort_columns=None,
+):
+    """# Import a 10x Image Dataset
+    
+    Pixel-to-micron: ???"""
+    magnification = 10
+    dataset = ShapeDataset(
+        filename,
+        batch_size=batch_size,
+        shuffle=shuffle,
+        pre_scale=magnification,
+        val_split=val_split,
+        scaler=scaler,
+        sort_columns=sort_columns,
+    )
+    return dataset
+
+
+def import_20x(
+    filename,
+    magnification=10,
+    batch_size=None,
+    shuffle=False,
+    val_split=0.0,
+    scaler=None,
+    sort_columns=None,
+):
+    """# Import a 20x Image Dataset
+    
+    Pixel-to-micron: ???"""
+    magnification = 20
+    dataset = ShapeDataset(
+        filename,
+        batch_size=batch_size,
+        shuffle=shuffle,
+        pre_scale=magnification,
+        val_split=val_split,
+        scaler=scaler,
+        sort_columns=sort_columns,
+    )
+    return dataset
+
+
+def import_dataset(
+    filename,
+    magnification,
+    batch_size=None,
+    shuffle=False,
+    val_split=0.0,
+    scaler=None,
+    sort_columns=None,
+):
+    """# Import a dataset
+
+    Requires a magnificaiton to be specified"""
+    dataset = ShapeDataset(
+        filename,
+        pre_scale=magnification,
+        batch_size=batch_size,
+        shuffle=shuffle,
+        val_split=val_split,
+        scaler=scaler,
+        sort_columns=sort_columns,
+    )
+    return dataset
+
+
+def import_full_dataset(fname, magnification=20, scaler=None):
+    """# Import a Full Dataset
+
+    If a classification file exists(.txt with a 'Class' header and 'frame','cellnumber' headers), also import it"""
+    from os.path import isfile
+    import pandas as pd
+    import numpy as np
+
+    cfname = fname
+    tfname = cfname[:-3] + "txt"
+    columns = [
+        "frame",
+        "cellnumber",
+        "x-cent",
+        "y-cent",
+        "actinedge",
+        "filopodia",
+        "bleb",
+        "lamellipodia",
+    ]
+    if isfile(tfname):
+        dataset = import_dataset(cfname, magnification=magnification, scaler=scaler)
+        class_df = np.loadtxt(tfname, skiprows=1)
+        class_df = pd.DataFrame(class_df, columns=columns)
+        full_df = pd.merge(
+            dataset.dataframe,
+            class_df,
+            left_on=["Frames", "CellNum"],
+            right_on=["frame", "cellnumber"],
+        )
+        full_df["Class"] = np.argmax(
+            class_df[["actinedge", "filopodia", "bleb", "lamellipodia"]].to_numpy(),
+            axis=-1,
+        )
+        dataset.labels = full_df["Class"].to_numpy()
+    else:
+        dataset = import_dataset(cfname, magnification=magnification, scaler=scaler)
+        full_df = dataset.dataframe
+    dataset.dataframe = full_df
+    dataset.filter_off()
+    return dataset
diff --git a/code/sunlab/common/distribution/__init__.py b/code/sunlab/common/distribution/__init__.py
new file mode 100644
index 0000000..a23cb0c
--- /dev/null
+++ b/code/sunlab/common/distribution/__init__.py
@@ -0,0 +1,7 @@
+from .gaussian_distribution import *
+from .x_gaussian_distribution import *
+from .o_gaussian_distribution import *
+from .s_gaussian_distribution import *
+from .uniform_distribution import *
+from .symmetric_uniform_distribution import *
+from .swiss_roll_distribution import *
diff --git a/code/sunlab/common/distribution/adversarial_distribution.py b/code/sunlab/common/distribution/adversarial_distribution.py
new file mode 100644
index 0000000..675c00e
--- /dev/null
+++ b/code/sunlab/common/distribution/adversarial_distribution.py
@@ -0,0 +1,35 @@
+class AdversarialDistribution:
+    """# Distribution Class to use in Adversarial Autoencoder
+
+    For any distribution to be implemented, make sure to ensure each of the
+    methods are implemented"""
+
+    def __init__(self, N):
+        """# Initialize the distribution for N-dimensions"""
+        self.dims = N
+        return
+
+    def get_full_name(self):
+        """# Return a human-readable name of the distribution"""
+        return self.full_name
+
+    def get_name(self):
+        """# Return a shortened name of the distribution
+
+        Preferrably, the name should include characters that can be included in
+        a file name"""
+        return self.name
+
+    def __str__(self):
+        """# Returns the short name"""
+        return self.get_name()
+
+    def __repr__(self):
+        """# Returns the short name"""
+        return self.get_name()
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use `dist(...)`"""
+        raise NotImplementedError("This distribution has not been implemented yet")
diff --git a/code/sunlab/common/distribution/gaussian_distribution.py b/code/sunlab/common/distribution/gaussian_distribution.py
new file mode 100644
index 0000000..e478ab6
--- /dev/null
+++ b/code/sunlab/common/distribution/gaussian_distribution.py
@@ -0,0 +1,23 @@
+from .adversarial_distribution import *
+
+
+class GaussianDistribution(AdversarialDistribution):
+    """# Gaussian Distribution"""
+
+    def __init__(self, N):
+        """# Gaussian Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        self.full_name = f"{N}-Dimensional Gaussian Distribution"
+        self.name = "G"
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use gauss(N1,...,Nm)"""
+        import numpy as np
+
+        return np.random.multivariate_normal(
+            mean=np.zeros(self.dims), cov=np.eye(self.dims), size=[*args]
+        )
diff --git a/code/sunlab/common/distribution/o_gaussian_distribution.py b/code/sunlab/common/distribution/o_gaussian_distribution.py
new file mode 100644
index 0000000..1222ca1
--- /dev/null
+++ b/code/sunlab/common/distribution/o_gaussian_distribution.py
@@ -0,0 +1,38 @@
+from .adversarial_distribution import *
+
+
+class OGaussianDistribution(AdversarialDistribution):
+    """# O Gaussian Distribution"""
+
+    def __init__(self, N):
+        """# O Gaussian Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        assert self.dims == 2, "This Distribution only Supports 2-Dimensions"
+        self.full_name = "2-Dimensional O-Gaussian Distribution"
+        self.name = "OG"
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use xgauss(case_count)"""
+        import numpy as np
+
+        assert len(args) == 1, "Only 1 argument supported"
+        N = args[0]
+        sample_base = np.zeros((4 * N, 2))
+        sample_base[0 * N : (0 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, 1], cov=[[1, 0], [0, 1]], size=[N]
+        )
+        sample_base[1 * N : (1 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, -1], cov=[[1, 0], [0, 1]], size=[N]
+        )
+        sample_base[2 * N : (2 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, 1], cov=[[1, 0], [0, 1]], size=[N]
+        )
+        sample_base[3 * N : (3 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, -1], cov=[[1, 0], [0, 1]], size=[N]
+        )
+        np.random.shuffle(sample_base)
+        return sample_base[:N, :]
diff --git a/code/sunlab/common/distribution/s_gaussian_distribution.py b/code/sunlab/common/distribution/s_gaussian_distribution.py
new file mode 100644
index 0000000..cace57f
--- /dev/null
+++ b/code/sunlab/common/distribution/s_gaussian_distribution.py
@@ -0,0 +1,40 @@
+from .adversarial_distribution import *
+
+
+class SGaussianDistribution(AdversarialDistribution):
+    """# S Gaussian Distribution"""
+
+    def __init__(self, N, scale=0):
+        """# S Gaussian Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        assert self.dims == 2, "This Distribution only Supports 2-Dimensions"
+        self.full_name = "2-Dimensional S-Gaussian Distribution"
+        self.name = "SG"
+        self.scale = scale
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use xgauss(case_count)"""
+        import numpy as np
+
+        assert len(args) == 1, "Only 1 argument supported"
+        N = args[0]
+        sample_base = np.zeros((4 * N, 2))
+        scale = self.scale
+        sample_base[0 * N : (0 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, 1], cov=[[1, scale], [scale, 1]], size=[N]
+        )
+        sample_base[1 * N : (1 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, -1], cov=[[1, scale], [scale, 1]], size=[N]
+        )
+        sample_base[2 * N : (2 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, 1], cov=[[1, -scale], [-scale, 1]], size=[N]
+        )
+        sample_base[3 * N : (3 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, -1], cov=[[1, -scale], [-scale, 1]], size=[N]
+        )
+        np.random.shuffle(sample_base)
+        return sample_base[:N, :]
diff --git a/code/sunlab/common/distribution/swiss_roll_distribution.py b/code/sunlab/common/distribution/swiss_roll_distribution.py
new file mode 100644
index 0000000..613bfc5
--- /dev/null
+++ b/code/sunlab/common/distribution/swiss_roll_distribution.py
@@ -0,0 +1,42 @@
+from .adversarial_distribution import *
+
+
+class SwissRollDistribution(AdversarialDistribution):
+    """# Swiss Roll Distribution"""
+
+    def __init__(self, N, scaling_factor=0.25, noise_level=0.15):
+        """# Swiss Roll Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        assert (self.dims == 2) or (
+            self.dims == 3
+        ), "This Distribution only Supports 2,3-Dimensions"
+        self.full_name = f"{self.dims}-Dimensional Swiss Roll Distribution Distribution"
+        self.name = f"SR{self.dims}"
+        self.noise_level = noise_level
+        self.scale = scaling_factor
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use xgauss(case_count)"""
+        import numpy as np
+
+        assert len(args) == 1, "Only 1 argument supported"
+        N = args[0]
+        noise = self.noise_level
+        scaling_factor = self.scale
+
+        t = 3 * np.pi / 2 * (1 + 2 * np.random.rand(1, N))
+        h = 21 * np.random.rand(1, N)
+        RANDOM = np.random.randn(3, N) * noise
+        data = (
+            np.concatenate(
+                (scaling_factor * t * np.cos(t), h, scaling_factor * t * np.sin(t))
+            )
+            + RANDOM
+        )
+        if self.dims == 2:
+            return data.T[:, [0, 2]]
+        return data.T[:, [0, 2, 1]]
diff --git a/code/sunlab/common/distribution/symmetric_uniform_distribution.py b/code/sunlab/common/distribution/symmetric_uniform_distribution.py
new file mode 100644
index 0000000..c3a4db0
--- /dev/null
+++ b/code/sunlab/common/distribution/symmetric_uniform_distribution.py
@@ -0,0 +1,21 @@
+from .adversarial_distribution import *
+
+
+class SymmetricUniformDistribution(AdversarialDistribution):
+    """# Symmetric Uniform Distribution on [-1, 1)"""
+
+    def __init__(self, N):
+        """# Symmetric Uniform Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        self.full_name = f"{N}-Dimensional Symmetric Uniform Distribution"
+        self.name = "SU"
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use suniform(N1,...,Nm)"""
+        import numpy as np
+
+        return np.random.rand(*args, self.dims) * 2.0 - 1.0
diff --git a/code/sunlab/common/distribution/uniform_distribution.py b/code/sunlab/common/distribution/uniform_distribution.py
new file mode 100644
index 0000000..3e23e67
--- /dev/null
+++ b/code/sunlab/common/distribution/uniform_distribution.py
@@ -0,0 +1,21 @@
+from .adversarial_distribution import *
+
+
+class UniformDistribution(AdversarialDistribution):
+    """# Uniform Distribution on [0, 1)"""
+
+    def __init__(self, N):
+        """# Uniform Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        self.full_name = f"{N}-Dimensional Uniform Distribution"
+        self.name = "U"
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use uniform(N1,...,Nm)"""
+        import numpy as np
+
+        return np.random.rand(*args, self.dims)
diff --git a/code/sunlab/common/distribution/x_gaussian_distribution.py b/code/sunlab/common/distribution/x_gaussian_distribution.py
new file mode 100644
index 0000000..b4330aa
--- /dev/null
+++ b/code/sunlab/common/distribution/x_gaussian_distribution.py
@@ -0,0 +1,38 @@
+from .adversarial_distribution import *
+
+
+class XGaussianDistribution(AdversarialDistribution):
+    """# X Gaussian Distribution"""
+
+    def __init__(self, N):
+        """# X Gaussian Distribution Initialization
+
+        Initializes the name and dimensions"""
+        super().__init__(N)
+        assert self.dims == 2, "This Distribution only Supports 2-Dimensions"
+        self.full_name = "2-Dimensional X-Gaussian Distribution"
+        self.name = "XG"
+
+    def __call__(self, *args):
+        """# Magic method when calling the distribution
+
+        This method is going to be called when you use xgauss(case_count)"""
+        import numpy as np
+
+        assert len(args) == 1, "Only 1 argument supported"
+        N = args[0]
+        sample_base = np.zeros((4 * N, 2))
+        sample_base[0 * N : (0 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, 1], cov=[[1, 0.7], [0.7, 1]], size=[N]
+        )
+        sample_base[1 * N : (1 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, -1], cov=[[1, 0.7], [0.7, 1]], size=[N]
+        )
+        sample_base[2 * N : (2 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[-1, 1], cov=[[1, -0.7], [-0.7, 1]], size=[N]
+        )
+        sample_base[3 * N : (3 + 1) * N, :] = np.random.multivariate_normal(
+            mean=[1, -1], cov=[[1, -0.7], [-0.7, 1]], size=[N]
+        )
+        np.random.shuffle(sample_base)
+        return sample_base[:N, :]
diff --git a/code/sunlab/common/mathlib/__init__.py b/code/sunlab/common/mathlib/__init__.py
new file mode 100644
index 0000000..9b5ed21
--- /dev/null
+++ b/code/sunlab/common/mathlib/__init__.py
@@ -0,0 +1 @@
+from .base import *
diff --git a/code/sunlab/common/mathlib/base.py b/code/sunlab/common/mathlib/base.py
new file mode 100644
index 0000000..38ab14c
--- /dev/null
+++ b/code/sunlab/common/mathlib/base.py
@@ -0,0 +1,57 @@
+import numpy as np
+
+
+def angle(a, b):
+    """# Get Angle Between Row Vectors"""
+    from numpy import arctan2, pi
+
+    theta_a = arctan2(a[:, 1], a[:, 0])
+    theta_b = arctan2(b[:, 1], b[:, 0])
+    d_theta = theta_b - theta_a
+    assert (-pi <= d_theta) and (d_theta <= pi), "Theta difference outside of [-π,π]"
+    return d_theta
+
+
+def normalize(column):
+    """# Normalize Column Vector"""
+    from numpy.linalg import norm
+
+    return column / norm(column, axis=0)
+
+
+def winding(xy_grid, trajectory_start, trajectory_end):
+    """# Get Winding Number on Grid"""
+    from numpy import zeros, cross, clip, arcsin
+
+    trajectories = trajectory_end - trajectory_start
+    winding = zeros((xy_grid.shape[0]))
+    for idx, trajectory in enumerate(trajectories):
+        r = xy_grid - trajectory_start[idx]
+        cross = cross(normalize(trajectory), normalize(r))
+        cross = clip(cross, -1, 1)
+        theta = arcsin(cross)
+        winding += theta
+    return winding
+
+
+def vorticity(xy_grid, trajectory_start, trajectory_end):
+    """# Get Vorticity Number on Grid"""
+    from numpy import zeros, cross
+
+    trajectories = trajectory_end - trajectory_start
+    vorticity = zeros((xy_grid.shape[0]))
+    for idx, trajectory in enumerate(trajectories):
+        r = xy_grid - trajectory_start[idx]
+        vorticity += cross(normalize(trajectory), normalize(r))
+    return vorticity
+
+
+def data_range(data):
+    """# Get the range of values for each row"""
+    from numpy import min, max
+
+    return min(data, axis=0), max(data, axis=0)
+
+
+np.normalize = normalize
+np.range = data_range
diff --git a/code/sunlab/common/mathlib/lyapunov.py b/code/sunlab/common/mathlib/lyapunov.py
new file mode 100644
index 0000000..3c747f1
--- /dev/null
+++ b/code/sunlab/common/mathlib/lyapunov.py
@@ -0,0 +1,54 @@
+def trajectory_to_distances(x):
+    """X: [N,N_t,N_d]
+    ret [N,N_t]"""
+    from numpy import zeros
+    from numpy.linalg import norm
+    from itertools import product, combinations
+
+    x = [x[idx, ...] for idx in range(x.shape[0])]
+    pairwise_trajectories = combinations(x, 2)
+    _N_COMB = len(list(pairwise_trajectories))
+    N_max = x[0].shape[0]
+    distances = zeros((_N_COMB, N_max))
+    pairwise_trajectories = combinations(x, 2)
+    for idx, (a_t, b_t) in enumerate(pairwise_trajectories):
+        distances[idx, :] = norm(a_t[:N_max, :] - b_t[:N_max, :], axis=-1)
+    return distances
+
+
+def Lyapunov_d(X):
+    """X: [N,N_t]
+    λ_n = ln(|dX_n|/|dX_0|)/n; n = [1,2,...]"""
+    from numpy import zeros, log, repeat
+
+    Y = zeros((X.shape[0], X.shape[1] - 1))
+    Y = log(X[:, 1:] / repeat([X[:, 0]], Y.shape[1], axis=0).T) / (
+        repeat([range(Y.shape[1])], Y.shape[0], axis=0) + 1
+    )
+    return Y
+
+
+def Lyapunov_t(X):
+    """X: [N,N_t,N_d]"""
+    return Lyapunov_d(trajectory_to_distances(X))
+
+
+Lyapunov = Lyapunov_d
+
+
+def RelativeDistance_d(X):
+    """X: [N,N_t]
+    λ_n = ln(|dX_n|/|dX_0|)/n; n = [1,2,...]"""
+    from numpy import zeros, log, repeat
+
+    Y = zeros((X.shape[0], X.shape[1] - 1))
+    Y = log(X[:, 1:] / repeat([X[:, 0]], Y.shape[1], axis=0).T)
+    return Y
+
+
+def RelativeDistance_t(X):
+    """X: [N,N_t,N_d]"""
+    return RelativeDistance_d(trajectory_to_distances(X))
+
+
+RelativeDistance = RelativeDistance_d
diff --git a/code/sunlab/common/mathlib/random_walks.py b/code/sunlab/common/mathlib/random_walks.py
new file mode 100644
index 0000000..3aa3bcb
--- /dev/null
+++ b/code/sunlab/common/mathlib/random_walks.py
@@ -0,0 +1,83 @@
+def get_levy_flight(T=50, D=2, t0=0.1, alpha=3, periodic=False):
+    from numpy import vstack
+    from mistree import get_levy_flight as get_flight
+
+    if D == 2:
+        x, y = get_flight(T, mode="2D", periodic=periodic, t_0=t0, alpha=alpha)
+        xy = vstack([x, y]).T
+    elif D == 3:
+        x, y, z = get_flight(T, mode="3D", periodic=periodic, t_0=t0, alpha=alpha)
+        xy = vstack([x, y, z]).T
+    else:
+        raise ValueError(f"Dimension {D} not supported!")
+    return xy
+
+
+def get_levy_flights(N=10, T=50, D=2, t0=0.1, alpha=3, periodic=False):
+    from numpy import moveaxis, array
+
+    trajectories = []
+    for _ in range(N):
+        xy = get_levy_flight(T=T, D=D, t0=t0, alpha=alpha, periodic=periodic)
+        trajectories.append(xy)
+    return moveaxis(array(trajectories), 0, 1)
+
+
+def get_jitter_levy_flights(
+    N=10, T=50, D=2, t0=0.1, alpha=3, periodic=False, noise=5e-2
+):
+    from numpy.random import randn
+
+    trajectories = get_levy_flights(
+        N=N, T=T, D=D, t0=t0, alpha=alpha, periodic=periodic
+    )
+    return trajectories + randn(*trajectories.shape) * noise
+
+
+def get_gaussian_random_walk(T=50, D=2, R=5, step_size=0.5, soft=None):
+    from numpy import array, sin, cos, exp, zeros, pi
+    from numpy.random import randn, uniform, rand
+    from numpy.linalg import norm
+
+    def is_in(x, R=1):
+        from numpy.linalg import norm
+
+        return norm(x) < R
+
+    X = zeros((T, D))
+    for t in range(1, T):
+        while True:
+            if D == 2:
+                angle = uniform(0, pi * 2)
+                step = randn(1) * step_size
+                X[t, :] = X[t - 1, :] + array([cos(angle), sin(angle)]) * step
+            else:
+                X[t, :] = X[t - 1, :] + randn(D) / D * step_size
+            if soft is None:
+                if is_in(X[t, :], R):
+                    break
+            elif rand() < exp(-(norm(X[t, :]) - R) * soft):
+                break
+    return X
+
+
+def get_gaussian_random_walks(N=10, T=50, D=2, R=5, step_size=0.5, soft=None):
+    from numpy import moveaxis, array
+
+    trajectories = []
+    for _ in range(N):
+        xy = get_gaussian_random_walk(T=T, D=D, R=R, step_size=step_size, soft=soft)
+        trajectories.append(xy)
+    return moveaxis(array(trajectories), 0, 1)
+
+
+def get_gaussian_sample(T=50, D=2):
+    from numpy.random import randn
+
+    return randn(T, D)
+
+
+def get_gaussian_samples(N=10, T=50, D=2, R=5, step_size=0.5):
+    from numpy.random import randn
+
+    return randn(T, N, D)
diff --git a/code/sunlab/common/plotting/__init__.py b/code/sunlab/common/plotting/__init__.py
new file mode 100644
index 0000000..d6873aa
--- /dev/null
+++ b/code/sunlab/common/plotting/__init__.py
@@ -0,0 +1,2 @@
+from .colors import *
+from .base import *
diff --git a/code/sunlab/common/plotting/base.py b/code/sunlab/common/plotting/base.py
new file mode 100644
index 0000000..aaf4a94
--- /dev/null
+++ b/code/sunlab/common/plotting/base.py
@@ -0,0 +1,270 @@
+from matplotlib import pyplot as plt
+
+
+def blank_plot(_plt=None, _xticks=False, _yticks=False):
+    """# Remove Plot Labels"""
+    if _plt is None:
+        _plt = plt
+    _plt.xlabel("")
+    _plt.ylabel("")
+    _plt.title("")
+    tick_params = {
+        "which": "both",
+        "bottom": _xticks,
+        "left": _yticks,
+        "right": False,
+        "labelleft": False,
+        "labelbottom": False,
+    }
+    _plt.tick_params(**tick_params)
+    for child in plt.gcf().get_children():
+        if child._label == "<colorbar>":
+            child.set_yticks([])
+    axs = _plt.gcf().get_axes()
+    try:
+        axs = axs.flatten()
+    except:
+        ...
+    for ax in axs:
+        ax.set_xlabel("")
+        ax.set_ylabel("")
+        ax.set_title("")
+        ax.tick_params(**tick_params)
+
+
+def save_plot(name, _plt=None, _xticks=False, _yticks=False, tighten=True):
+    """# Save Plot in Multiple Formats"""
+    assert type(name) == str, "Name must be string"
+    from os.path import dirname
+    from os import makedirs
+
+    makedirs(dirname(name), exist_ok=True)
+    if _plt is None:
+        from matplotlib import pyplot as plt
+        _plt = plt
+    _plt.savefig(name + ".png", dpi=1000)
+    blank_plot(_plt, _xticks=_xticks, _yticks=_yticks)
+    if tighten:
+        from matplotlib import pyplot as plt
+        plt.tight_layout()
+    _plt.savefig(name + ".pdf")
+    _plt.savefig(name + ".svg")
+
+
+def scatter_2d(data_2d, labels=None, _plt=None, **matplotlib_kwargs):
+    """# Scatter 2d Data
+
+    - data_2d: 2d-dataset to plot
+    - labels: labels for each case
+    - _plt: Optional specific plot to transform"""
+    from .colors import Pcolor
+
+    if _plt is None:
+        _plt = plt
+
+    def _filter(data, labels=None, _filter_on=None):
+        if labels is None:
+            return data, False
+        else:
+            return data[labels == _filter_on], True
+
+    for _class in [2, 3, 1, 0]:
+        local_data, has_color = _filter(data_2d, labels, _class)
+        if has_color:
+            _plt.scatter(
+                local_data[:, 0],
+                local_data[:, 1],
+                color=Pcolor[_class],
+                **matplotlib_kwargs
+            )
+        else:
+            _plt.scatter(local_data[:, 0], local_data[:, 1], **matplotlib_kwargs)
+            break
+    return _plt
+
+
+def plot_contour(two_d_mask, color="black", color_map=None, raise_error=False):
+    """# Plot Contour of Mask"""
+    from matplotlib.pyplot import contour
+    from numpy import mgrid
+
+    z = two_d_mask
+    x, y = mgrid[: z.shape[1], : z.shape[0]]
+    if color_map is not None:
+        try:
+            color = color_map(color)
+        except Exception as e:
+            if raise_error:
+                raise e
+    try:
+        contour(x, y, z.T, colors=color, linewidth=0.5)
+    except Exception as e:
+        if raise_error:
+            raise e
+
+
+def gaussian_smooth_plot(
+    xy,
+    sigma=0.1,
+    extent=[-1, 1, -1, 1],
+    grid_n=100,
+    grid=None,
+    do_normalize=True,
+):
+    """# Plot Data with Gaussian Smoothening around point"""
+    from numpy import array, ndarray, linspace, meshgrid, zeros_like
+    from numpy import pi, sqrt, exp
+    from numpy.linalg import norm
+
+    if not type(xy) == ndarray:
+        xy = array(xy)
+    if grid is not None:
+        XY = grid
+    else:
+        X = linspace(extent[0], extent[1], grid_n)
+        Y = linspace(extent[2], extent[3], grid_n)
+        XY = array(meshgrid(X, Y)).T
+    smoothed = zeros_like(XY[:, :, 0])
+    factor = 1
+    if do_normalize:
+        factor = (sqrt(2 * pi) * sigma) ** 2.
+    if len(xy.shape) == 1:
+        smoothed = exp(-((norm(xy - XY, axis=-1) / (sqrt(2) * sigma)) ** 2.0)) / factor
+    else:
+        try:
+            from tqdm.notebook import tqdm
+        except Exception:
+
+            def tqdm(x):
+                return x
+
+        for i in tqdm(range(xy.shape[0])):
+            if xy.shape[-1] == 2:
+                smoothed += (
+                    exp(-((norm((xy[i, :] - XY), axis=-1) / (sqrt(2) * sigma)) ** 2.0))
+                    / factor
+                )
+            elif xy.shape[-1] == 3:
+                smoothed += (
+                    exp(-((norm((xy[i, :2] - XY), axis=-1) / (sqrt(2) * sigma)) ** 2.0))
+                    / factor
+                    * xy[i, 2]
+                )
+    return smoothed, XY
+
+
+def plot_grid_data(xy_grid, data_grid, cbar=False, _plt=None, _cmap="RdBu", grid_min=1):
+    """# Plot Gridded Data"""
+    from numpy import nanmin, nanmax
+    from matplotlib.colors import TwoSlopeNorm
+
+    if _plt is None:
+        _plt = plt
+    norm = TwoSlopeNorm(
+        vmin=nanmin([-grid_min, nanmin(data_grid)]),
+        vcenter=0,
+        vmax=nanmax([grid_min, nanmax(data_grid)]),
+    )
+    _plt.pcolor(xy_grid[:, :, 0], xy_grid[:, :, 1], data_grid, cmap="RdBu", norm=norm)
+    if cbar:
+        _plt.colorbar()
+
+
+def plot_winding(xy_grid, winding_grid, cbar=False, _plt=None):
+    plot_grid_data(xy_grid, winding_grid, cbar=cbar, _plt=_plt, grid_min=1e-5)
+
+
+def plot_vorticity(xy_grid, vorticity_grid, cbar=False, save=False, _plt=None):
+    plot_grid_data(xy_grid, vorticity_grid, cbar=cbar, _plt=_plt, grid_min=1e-1)
+
+
+plt.blank = lambda: blank_plot(plt)
+plt.scatter2d = lambda data, labels=None, **matplotlib_kwargs: scatter_2d(
+    data, labels, plt, **matplotlib_kwargs
+)
+plt.save = save_plot
+
+
+def interpolate_points(df, columns=["Latent-0", "Latent-1"], kind="quadratic", N=500):
+    """# Interpolate points"""
+    from scipy.interpolate import interp1d
+    import numpy as np
+
+    points = df[columns].to_numpy()
+    distance = np.cumsum(np.sqrt(np.sum(np.diff(points, axis=0) ** 2, axis=1)))
+    distance = np.insert(distance, 0, 0) / distance[-1]
+    interpolator = interp1d(distance, points, kind=kind, axis=0)
+    alpha = np.linspace(0, 1, N)
+    interpolated_points = interpolator(alpha)
+    return interpolated_points.reshape(-1, 1, 2)
+
+
+def plot_trajectory(
+    df,
+    Fm=24,
+    FM=96,
+    interpolate=False,
+    interpolation_kind="quadratic",
+    interpolation_N=500,
+    columns=["Latent-0", "Latent-1"],
+    frame_column="Frames",
+    alpha=0.8,
+    lw=4,
+    _plt=None,
+    _z=None,
+):
+    """# Plot Trajectories
+
+    Interpolation possible"""
+    import numpy as np
+    from matplotlib.collections import LineCollection
+    import matplotlib as mpl
+
+    if _plt is None:
+        _plt = plt
+    if type(_plt) == mpl.axes._axes.Axes:
+        _ca = _plt
+    else:
+        try:
+            _ca = _plt.gca()
+        except:
+            _ca = _plt
+    X = df[columns[0]]
+    Y = df[columns[1]]
+    fm, fM = np.min(df[frame_column]), np.max(df[frame_column])
+
+    if interpolate:
+        if interpolation_kind == "cubic":
+            if len(df) <= 3:
+                return
+        elif interpolation_kind == "quadratic":
+            if len(df) <= 2:
+                return
+        else:
+            if len(df) <= 1:
+                return
+        points = interpolate_points(
+            df, kind=interpolation_kind, columns=columns, N=interpolation_N
+        )
+    else:
+        points = np.array([X, Y]).T.reshape(-1, 1, 2)
+
+    segments = np.concatenate([points[:-1], points[1:]], axis=1)
+    lc = LineCollection(
+        segments,
+        cmap=plt.get_cmap("plasma"),
+        norm=mpl.colors.Normalize(Fm, FM),
+    )
+    if _z is not None:
+        from mpl_toolkits.mplot3d.art3d import line_collection_2d_to_3d
+
+        if interpolate:
+            _z = _z  # TODO: Interpolate
+        line_collection_2d_to_3d(lc, _z)
+    lc.set_array(np.linspace(fm, fM, points.shape[0]))
+    lc.set_linewidth(lw)
+    lc.set_alpha(alpha)
+    _ca.add_collection(lc)
+    _ca.autoscale()
+    _ca.margins(0.04)
+    return lc
diff --git a/code/sunlab/common/plotting/colors.py b/code/sunlab/common/plotting/colors.py
new file mode 100644
index 0000000..c4fc727
--- /dev/null
+++ b/code/sunlab/common/plotting/colors.py
@@ -0,0 +1,38 @@
+class PhenotypeColors:
+    """# Phenotype Colorings
+
+    Standardization for the different phenotype colors"""
+
+    def __init__(self):
+        """# Empty Construtor"""
+        pass
+
+    def get_basic_colors(self, transition=False):
+        """# Return the Color Names
+
+        - transition: Returns the color for the transition class too"""
+        if transition:
+            return ["yellow", "purple", "green", "blue", "cyan"]
+        return ["yellow", "purple", "green", "blue"]
+
+    def get_colors(self, transition=False):
+        """# Return the Color Names
+
+        - transition: Returns the color for the transition class too"""
+        if transition:
+            return ["#ffff00", "#ff3cfa", "#11f309", "#213ff0", "cyan"]
+        return ["#ffff00", "#ff3cfa", "#11fe09", "#213ff0"]
+
+    def get_colormap(self, transition=False):
+        """# Return the Matplotlib Colormap
+
+        - transition: Returns the color for the transition class too"""
+        from matplotlib.colors import ListedColormap as LC
+
+        return LC(self.get_colors(transition))
+
+
+# Basic Exports
+Pcolor = PhenotypeColors().get_colors()
+Pmap = PhenotypeColors().get_colormap()
+Pmapx = PhenotypeColors().get_colormap(True)
diff --git a/code/sunlab/common/scaler/__init__.py b/code/sunlab/common/scaler/__init__.py
new file mode 100644
index 0000000..2a2281a
--- /dev/null
+++ b/code/sunlab/common/scaler/__init__.py
@@ -0,0 +1,2 @@
+from .max_abs_scaler import *
+from .quantile_scaler import *
diff --git a/code/sunlab/common/scaler/adversarial_scaler.py b/code/sunlab/common/scaler/adversarial_scaler.py
new file mode 100644
index 0000000..7f61725
--- /dev/null
+++ b/code/sunlab/common/scaler/adversarial_scaler.py
@@ -0,0 +1,44 @@
+class AdversarialScaler:
+    """# Scaler Class to use in Adversarial Autoencoder
+
+    For any scaler to be implemented, make sure to ensure each of the methods
+    are implemented:
+    - __init__ (optional)
+    - init
+    - load
+    - save
+    - __call__"""
+
+    def __init__(self, base_directory):
+        """# Scaler initialization
+
+        - Initialize the base directory of the model where it will live"""
+        self.base_directory = base_directory
+
+    def init(self, data):
+        """# Scaler initialization
+
+        Initialize the scaler transformation with the data
+        Should always return self in subclasses"""
+        raise NotImplementedError("Scaler initialization has not been implemented yet")
+
+    def load(self):
+        """# Scaler loading
+
+        Load the data scaler model from a file
+        Should always return self in subclasses"""
+        raise NotImplementedError("Scaler loading has not been implemented yet")
+
+    def save(self):
+        """# Scaler saving
+
+        Save the data scaler model"""
+        raise NotImplementedError("Scaler saving has not been implemented yet")
+
+    def transform(self, *args, **kwargs):
+        """# Scale the given data"""
+        return self.__call__(*args, **kwargs)
+
+    def __call__(self, *args, **kwargs):
+        """# Scale the given data"""
+        raise NotImplementedError("Scaler has not been implemented yet")
diff --git a/code/sunlab/common/scaler/max_abs_scaler.py b/code/sunlab/common/scaler/max_abs_scaler.py
new file mode 100644
index 0000000..56ea589
--- /dev/null
+++ b/code/sunlab/common/scaler/max_abs_scaler.py
@@ -0,0 +1,48 @@
+from .adversarial_scaler import AdversarialScaler
+
+
+class MaxAbsScaler(AdversarialScaler):
+    """# MaxAbsScaler
+
+    Scale the data based on the maximum-absolute value in each column"""
+
+    def __init__(self, base_directory):
+        """# MaxAbsScaler initialization
+
+        - Initialize the base directory of the model where it will live
+        - Initialize the scaler model"""
+        super().__init__(base_directory)
+        from sklearn.preprocessing import MaxAbsScaler as MAS
+
+        self.scaler_base = MAS()
+        self.scaler = None
+
+    def init(self, data):
+        """# Scaler initialization
+
+        Initialize the scaler transformation with the data"""
+        self.scaler = self.scaler_base.fit(data)
+        return self
+
+    def load(self):
+        """# Scaler loading
+
+        Load the data scaler model from a file"""
+        from pickle import load
+
+        with open(f"{self.base_directory}/portable/maxabs_scaler.pkl", "rb") as fhandle:
+            self.scaler = load(fhandle)
+        return self
+
+    def save(self):
+        """# Scaler saving
+
+        Save the data scaler model"""
+        from pickle import dump
+
+        with open(f"{self.base_directory}/portable/maxabs_scaler.pkl", "wb") as fhandle:
+            dump(self.scaler, fhandle)
+
+    def __call__(self, *args, **kwargs):
+        """# Scale the given data"""
+        return self.scaler.transform(*args, **kwargs)
diff --git a/code/sunlab/common/scaler/quantile_scaler.py b/code/sunlab/common/scaler/quantile_scaler.py
new file mode 100644
index 0000000..a0f53fd
--- /dev/null
+++ b/code/sunlab/common/scaler/quantile_scaler.py
@@ -0,0 +1,52 @@
+from .adversarial_scaler import AdversarialScaler
+
+
+class QuantileScaler(AdversarialScaler):
+    """# QuantileScaler
+
+    Scale the data based on the quantile distributions of each column"""
+
+    def __init__(self, base_directory):
+        """# QuantileScaler initialization
+
+        - Initialize the base directory of the model where it will live
+        - Initialize the scaler model"""
+        super().__init__(base_directory)
+        from sklearn.preprocessing import QuantileTransformer as QS
+
+        self.scaler_base = QS()
+        self.scaler = None
+
+    def init(self, data):
+        """# Scaler initialization
+
+        Initialize the scaler transformation with the data"""
+        self.scaler = self.scaler_base.fit(data)
+        return self
+
+    def load(self):
+        """# Scaler loading
+
+        Load the data scaler model from a file"""
+        from pickle import load
+
+        with open(
+            f"{self.base_directory}/portable/quantile_scaler.pkl", "rb"
+        ) as fhandle:
+            self.scaler = load(fhandle)
+        return self
+
+    def save(self):
+        """# Scaler saving
+
+        Save the data scaler model"""
+        from pickle import dump
+
+        with open(
+            f"{self.base_directory}/portable/quantile_scaler.pkl", "wb"
+        ) as fhandle:
+            dump(self.scaler, fhandle)
+
+    def __call__(self, *args, **kwargs):
+        """# Scale the given data"""
+        return self.scaler.transform(*args, **kwargs)
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