Merge version 0.2.0 into feature/plugin-architecture.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.1-rc0
+current_version = 0.2.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
@@ -19,3 +19,4 @@ values =
 
 [bumpversion:file:./prototorch/__init__.py]
 
+[bumpversion:file:./docs/source/conf.py]

.readthedocs.yml

@@ -0,0 +1,27 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+# mkdocs:
+#   configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.8
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - all

README.md

@@ -45,22 +45,8 @@ pip install -e .[all]
 
 ## Documentation
 
-The documentation is available at <https://prototorch.readthedocs.io/en/latest/>
-
-## Usage
-
-### For researchers
-ProtoTorch is modular. It is very easy to use the modular pieces provided by
-ProtoTorch, like the layers, losses, callbacks and metrics to build your own
-prototype-based(instance-based) models. These pieces blend-in seamlessly with
-Keras allowing you to mix and match the modules from ProtoFlow with other
-modules in `torch.nn`.
-
-### For engineers
-ProtoTorch comes prepackaged with many popular Learning Vector Quantization
-(LVQ)-like algorithms in a convenient API. If you would simply like to be able
-to use those algorithms to train large ML models on a GPU, ProtoTorch lets you
-do this without requiring a black-belt in high-performance Tensor computing.
+The documentation is available at <https://www.prototorch.ml/en/latest/>. Should
+that link not work try <https://prototorch.readthedocs.io/en/latest/>.
 
 ## Bibtex
 

RELEASE.md

@@ -1,5 +1,10 @@
 # ProtoTorch Releases
 
+## Release 0.2.0
+
+### Includes
+- Fixes in example scripts.
+
 ## Release 0.1.1-dev0
 
 ### Includes

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= python3 -m sphinx
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+  set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+  echo.
+  echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+  echo.installed, then set the SPHINXBUILD environment variable to point
+  echo.to the full path of the 'sphinx-build' executable. Alternatively you
+  echo.may add the Sphinx directory to PATH.
+  echo.
+  echo.If you don't have Sphinx installed, grab it from
+  echo.http://sphinx-doc.org/
+  exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,4 @@
+torch==1.6.0
+matplotlib==3.1.2
+sphinx_rtd_theme==0.5.0
+sphinxcontrib-katex==0.6.1

docs/source/api.rst

@@ -0,0 +1,28 @@
+.. ProtoFlow API Reference
+
+ProtoFlow API Reference
+======================================
+
+Datasets
+--------------------------------------
+.. automodule:: prototorch.datasets
+   :members:
+   :undoc-members:
+
+Functions
+--------------------------------------
+.. automodule:: prototorch.functions
+   :members:
+   :undoc-members:
+
+Modules
+--------------------------------------
+.. automodule:: prototorch.modules
+   :members:
+   :undoc-members:
+
+Utilities
+--------------------------------------
+.. automodule:: prototorch.utils
+   :members:
+   :undoc-members:

docs/source/conf.py

@@ -0,0 +1,180 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath("../../"))
+
+import sphinx_rtd_theme
+
+# -- Project information -----------------------------------------------------
+
+project = "ProtoTorch"
+copyright = "2021, Jensun Ravichandran"
+author = "Jensun Ravichandran"
+
+# The full version, including alpha/beta/rc tags
+#
+release = "0.2.0"
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+needs_sphinx = "1.6"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
+# ones.
+extensions = [
+    "recommonmark",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
+    "sphinxcontrib.katex",
+]
+
+# katex_prerender = True
+katex_prerender = False
+
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = [".rst", ".md"]
+
+# The master toctree document.
+master_doc = "index"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use. Choose from:
+# ["default", "emacs", "friendly", "colorful", "autumn", "murphy", "manni",
+#  "monokai", "perldoc", "pastie", "borland", "trac", "native", "fruity", "bw",
+#  "vim", "vs", "tango", "rrt", "xcode", "igor", "paraiso-light", "paraiso-dark",
+#  "lovelace", "algol", "algol_nu", "arduino", "rainbo w_dash", "abap",
+#  "solarized-dark", "solarized-light", "sas", "stata", "stata-light",
+#  "stata-dark", "inkpot"]
+pygments_style = "monokai"
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+# Disable docstring inheritance
+autodoc_inherit_docstrings = False
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# https://sphinx-themes.org/
+html_theme = "sphinx_rtd_theme"
+
+html_logo = "_static/img/horizontal-lockup.png"
+
+html_theme_options = {
+    "logo_only": True,
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
+    "style_external_links": False,
+    "style_nav_header_background": "#ffffff",
+    # Toc options
+    "collapse_navigation": True,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+html_css_files = [
+    "https://cdn.jsdelivr.net/npm/katex@0.11.1/dist/katex.min.css",
+]
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "protoflowdoc"
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ("letterpaper" or "a4paper").
+    #
+    # "papersize": "letterpaper",
+
+    # The font size ("10pt", "11pt" or "12pt").
+    #
+    # "pointsize": "10pt",
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # "preamble": "",
+
+    # Latex figure (float) alignment
+    #
+    # "figure_align": "htbp",
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, "prototorch.tex", "ProtoTorch Documentation",
+     "Jensun Ravichandran", "manual"),
+]
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "ProtoTorch", "ProtoTorch Documentation", [author], 1)]
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, "prototorch", "ProtoTorch Documentation", author, "prototorch",
+     "Prototype-based machine learning in PyTorch.",
+     "Miscellaneous"),
+]
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+}
+
+# -- Options for Epub output ----------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-epub-output
+
+epub_cover = ()
+version = release

docs/source/index.rst

@@ -0,0 +1,22 @@
+.. ProtoTorch documentation master file
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+About ProtoTorch
+================
+
+.. toctree::
+   :hidden:
+   :maxdepth: 3
+   :caption: Contents:
+
+   self
+   api
+
+ProtoTorch is a PyTorch-based Python toolbox for bleeding-edge
+research in prototype-based machine learning algorithms.
+
+Indices
+=======
+* :ref:`genindex`
+* :ref:`modindex`

examples/gtlvq_mnist.py

@@ -0,0 +1,162 @@
+"""
+ProtoTorch GTLVQ example using MNIST data.
+The GTLVQ is placed as an classification model on
+top of a CNN, considered as featurer extractor.
+Initialization of subpsace and prototypes in
+Siamnese fashion
+For more info about GTLVQ see:
+DOI:10.1109/IJCNN.2016.7727534
+"""
+
+import numpy as np
+import torch
+import torch.nn as nn
+import torchvision
+from torchvision import transforms
+from prototorch.modules.losses import GLVQLoss
+from prototorch.functions.helper import calculate_prototype_accuracy
+from prototorch.modules.models import GTLVQ
+
+# Parameters and options
+n_epochs = 50
+batch_size_train = 64
+batch_size_test = 1000
+learning_rate = 0.1
+momentum = 0.5
+log_interval = 10
+cuda = "cuda:1"
+random_seed = 1
+device = torch.device(cuda if torch.cuda.is_available() else 'cpu')
+
+# Configures reproducability
+torch.manual_seed(random_seed)
+np.random.seed(random_seed)
+
+# Prepare and preprocess the data
+train_loader = torch.utils.data.DataLoader(torchvision.datasets.MNIST(
+    './files/',
+    train=True,
+    download=True,
+    transform=torchvision.transforms.Compose(
+        [transforms.ToTensor(),
+         transforms.Normalize((0.1307, ), (0.3081, ))])),
+                                           batch_size=batch_size_train,
+                                           shuffle=True)
+
+test_loader = torch.utils.data.DataLoader(torchvision.datasets.MNIST(
+    './files/',
+    train=False,
+    download=True,
+    transform=torchvision.transforms.Compose(
+        [transforms.ToTensor(),
+         transforms.Normalize((0.1307, ), (0.3081, ))])),
+                                          batch_size=batch_size_test,
+                                          shuffle=True)
+
+
+# Define the GLVQ model plus appropriate feature extractor
+class CNNGTLVQ(torch.nn.Module):
+    def __init__(
+        self,
+        num_classes,
+        subspace_data,
+        prototype_data,
+        tangent_projection_type="local",
+        prototypes_per_class=2,
+        bottleneck_dim=128,
+    ):
+        super(CNNGTLVQ, self).__init__()
+
+        #Feature Extractor - Simple CNN
+        self.fe = nn.Sequential(nn.Conv2d(1, 32, 3, 1), nn.ReLU(),
+                                nn.Conv2d(32, 64, 3, 1), nn.ReLU(),
+                                nn.MaxPool2d(2), nn.Dropout(0.25),
+                                nn.Flatten(), nn.Linear(9216, bottleneck_dim),
+                                nn.Dropout(0.5), nn.LeakyReLU(),
+                                nn.LayerNorm(bottleneck_dim))
+
+        # Forward pass of subspace and prototype initialization data through feature extractor
+        subspace_data = self.fe(subspace_data)
+        prototype_data[0] = self.fe(prototype_data[0])
+
+        # Initialization of GTLVQ
+        self.gtlvq = GTLVQ(num_classes,
+                           subspace_data,
+                           prototype_data,
+                           tangent_projection_type=tangent_projection_type,
+                           feature_dim=bottleneck_dim,
+                           prototypes_per_class=prototypes_per_class)
+
+    def forward(self, x):
+        # Feature Extraction
+        x = self.fe(x)
+
+        # GTLVQ Forward pass
+        dis = self.gtlvq(x)
+        return dis
+
+
+# Get init data
+subspace_data = torch.cat(
+    [next(iter(train_loader))[0],
+     next(iter(test_loader))[0]])
+prototype_data = next(iter(train_loader))
+
+# Build the CNN GTLVQ  model
+model = CNNGTLVQ(10,
+                 subspace_data,
+                 prototype_data,
+                 tangent_projection_type="local",
+                 bottleneck_dim=128).to(device)
+
+# Optimize using SGD optimizer from `torch.optim`
+optimizer = torch.optim.Adam([{
+    'params': model.fe.parameters()
+}, {
+    'params': model.gtlvq.parameters()
+}],
+                             lr=learning_rate)
+criterion = GLVQLoss(squashing='sigmoid_beta', beta=10)
+
+# Training loop
+for epoch in range(n_epochs):
+    for batch_idx, (x_train, y_train) in enumerate(train_loader):
+        model.train()
+        x_train, y_train = x_train.to(device), y_train.to(device)
+        optimizer.zero_grad()
+
+        distances = model(x_train)
+        plabels = model.gtlvq.cls.prototype_labels.to(device)
+
+        # Compute loss.
+        loss = criterion([distances, plabels], y_train)
+        loss.backward()
+        optimizer.step()
+
+        # GTLVQ uses projected SGD, which means to orthogonalize the subspaces after every gradient update.
+        model.gtlvq.orthogonalize_subspace()
+
+        if batch_idx % log_interval == 0:
+            acc = calculate_prototype_accuracy(distances, y_train, plabels)
+            print(
+                f'Epoch: {epoch + 1:02d}/{n_epochs:02d} Epoch Progress: {100. * batch_idx / len(train_loader):02.02f} % Loss: {loss.item():02.02f} \
+              Train Acc: {acc.item():02.02f}')
+
+    # Test
+    with torch.no_grad():
+        model.eval()
+        correct = 0
+        total = 0
+        for x_test, y_test in test_loader:
+            x_test, y_test = x_test.to(device), y_test.to(device)
+            test_distances = model(torch.tensor(x_test))
+            test_plabels = model.gtlvq.cls.prototype_labels.to(device)
+            i = torch.argmin(test_distances, 1)
+            correct += torch.sum(y_test == test_plabels[i])
+            total += y_test.size(0)
+        print('Accuracy of the network on the test images: %d %%' %
+              (torch.true_divide(correct, total) * 100))
+
+# Save the model
+PATH = './glvq_mnist_model.pth'
+torch.save(model.state_dict(), PATH)

prototorch/__init__.py

@@ -3,14 +3,7 @@
 # #############################################
 # Core Setup
 # #############################################
-from importlib.metadata import version, PackageNotFoundError
-
-VERSION_FALLBACK = "uninstalled_version"
-try:
-    __version_core__ = version(__name__)
-except PackageNotFoundError:
-    __version_core__ = VERSION_FALLBACK
-    pass
+__version__ = "0.2.0"
 
 from prototorch import datasets, functions, modules
 
@@ -40,14 +33,14 @@ discovered_plugins = discover_plugins()
 locals().update(discovered_plugins)
 
 # Generate combines __version__ and __all__
-__version_plugins__ = "\n".join(
+version_plugins = "\n".join(
     [
         "- " + name + ": v" + plugin.__version__
         for name, plugin in discovered_plugins.items()
     ]
 )
-if __version_plugins__ != "":
-    __version_plugins__ = "\nPlugins: \n" + __version_plugins__
+if version_plugins != "":
+    version_plugins = "\nPlugins: \n" + version_plugins
 
-__version__ = "core: v" + __version_core__ + __version_plugins__
+version = "core: v" + __version__ + version_plugins
 __all__ = __all_core__ + list(discovered_plugins.keys())

prototorch/functions/distances.py

@@ -1,6 +1,8 @@
 """ProtoTorch distance functions."""
 
 import torch
+from prototorch.functions.helper import equal_int_shape, _int_and_mixed_shape, _check_shapes
+import numpy as np
 
 
 def squared_euclidean_distance(x, y):
@@ -71,5 +73,155 @@ def lomega_distance(x, y, omegas):
     return distances
 
 
+def euclidean_distance_matrix(x, y, squared=False, epsilon=1e-10):
+    r""" Computes an euclidean distanes matrix given two distinct vectors.
+    last dimension must be the vector dimension!
+    compute the distance via the identity of the dot product. This avoids the memory overhead due to the subtraction!
+
+    x.shape = (number_of_x_vectors, vector_dim)
+    y.shape = (number_of_y_vectors, vector_dim)
+
+    output: matrix of distances (number_of_x_vectors, number_of_y_vectors)
+    """
+    for tensor in [x, y]:
+        if tensor.ndim != 2:
+            raise ValueError(
+                'The tensor dimension must be two. You provide: tensor.ndim=' +
+                str(tensor.ndim) + '.')
+    if not equal_int_shape([tuple(x.shape)[1]], [tuple(y.shape)[1]]):
+        raise ValueError(
+            'The vector shape must be equivalent in both tensors. You provide: tuple(y.shape)[1]='
+            + str(tuple(x.shape)[1]) + ' and  tuple(y.shape)(y)[1]=' +
+            str(tuple(y.shape)[1]) + '.')
+
+    y = torch.transpose(y)
+
+    diss = torch.sum(x**2, axis=1,
+                     keepdims=True) - 2 * torch.dot(x, y) + torch.sum(
+                         y**2, axis=0, keepdims=True)
+
+    if not squared:
+        if epsilon == 0:
+            diss = torch.sqrt(diss)
+        else:
+            diss = torch.sqrt(torch.max(diss, epsilon))
+
+    return diss
+
+
+def tangent_distance(signals, protos, subspaces, squared=False, epsilon=1e-10):
+    r""" Tangent distances based on the tensorflow implementation of Sascha Saralajews
+    For more info about Tangen distances see DOI:10.1109/IJCNN.2016.7727534.
+    The subspaces is always assumed as transposed and must be orthogonal!
+    For local non sparse signals subspaces must be provided!
+    shape(signals): batch x proto_number x channels x dim1 x dim2 x ... x dimN
+    shape(protos): proto_number x dim1 x dim2 x ... x dimN
+    shape(subspaces): (optional [proto_number]) x prod(dim1 * dim2 * ... * dimN)  x prod(projected_atom_shape)
+    subspace should be orthogonalized
+    Pytorch implementation of Sascha Saralajew's tensorflow code.
+    Translation by Christoph Raab
+    """
+    signal_shape, signal_int_shape = _int_and_mixed_shape(signals)
+    proto_shape, proto_int_shape = _int_and_mixed_shape(protos)
+    subspace_int_shape = tuple(subspaces.shape)
+
+    # check if the shapes are correct
+    _check_shapes(signal_int_shape, proto_int_shape)
+
+    atom_axes = list(range(3, len(signal_int_shape)))
+    # for sparse signals, we use the memory efficient implementation
+    if signal_int_shape[1] == 1:
+        signals = torch.reshape(signals, [-1, np.prod(signal_shape[3:])])
+
+        if len(atom_axes) > 1:
+            protos = torch.reshape(protos, [proto_shape[0], -1])
+
+        if subspaces.ndim == 2:
+            # clean solution without map if the matrix_scope is global
+            projectors = torch.eye(subspace_int_shape[-2]) - torch.dot(
+                subspaces, torch.transpose(subspaces))
+
+            projected_signals = torch.dot(signals, projectors)
+            projected_protos = torch.dot(protos, projectors)
+
+            diss = euclidean_distance_matrix(projected_signals,
+                                             projected_protos,
+                                             squared=squared,
+                                             epsilon=epsilon)
+
+            diss = torch.reshape(
+                diss, [signal_shape[0], signal_shape[2], proto_shape[0]])
+
+            return torch.permute(diss, [0, 2, 1])
+
+        else:
+
+            # no solution without map possible --> memory efficient but slow!
+            projectors = torch.eye(subspace_int_shape[-2]) - torch.bmm(
+                subspaces,
+                subspaces)  #K.batch_dot(subspaces, subspaces, [2, 2])
+
+            projected_protos = (protos @ subspaces
+                                ).T  #K.batch_dot(projectors, protos, [1, 1]))
+
+            def projected_norm(projector):
+                return torch.sum(torch.dot(signals, projector)**2, axis=1)
+
+            diss = torch.transpose(map(projected_norm, projectors)) \
+                    - 2 * torch.dot(signals, projected_protos) \
+                    + torch.sum(projected_protos**2, axis=0, keepdims=True)
+
+            if not squared:
+                if epsilon == 0:
+                    diss = torch.sqrt(diss)
+                else:
+                    diss = torch.sqrt(torch.max(diss, epsilon))
+
+            diss = torch.reshape(
+                diss, [signal_shape[0], signal_shape[2], proto_shape[0]])
+
+            return torch.permute(diss, [0, 2, 1])
+
+    else:
+        signals = signals.permute([0, 2, 1] + atom_axes)
+
+        diff = signals - protos
+
+        # global tangent space
+        if subspaces.ndim == 2:
+            #Scope Projectors
+            projectors = subspaces  #
+
+            #Scope: Tangentspace Projections
+            diff = torch.reshape(
+                diff, (signal_shape[0] * signal_shape[2], signal_shape[1], -1))
+            projected_diff = diff @ projectors
+            projected_diff = torch.reshape(
+                projected_diff,
+                (signal_shape[0], signal_shape[2], signal_shape[1]) +
+                signal_shape[3:])
+
+            diss = torch.norm(projected_diff, 2, dim=-1)
+            return diss.permute([0, 2, 1])
+
+        # local tangent spaces
+        else:
+            # Scope: Calculate Projectors
+            projectors = subspaces
+
+            # Scope: Tangentspace Projections
+            diff = torch.reshape(
+                diff, (signal_shape[0] * signal_shape[2], signal_shape[1], -1))
+            diff = diff.permute([1, 0, 2])
+            projected_diff = torch.bmm(diff, projectors)
+            projected_diff = torch.reshape(
+                projected_diff,
+                (signal_shape[1], signal_shape[0], signal_shape[2]) +
+                signal_shape[3:])
+
+            diss = torch.norm(projected_diff, 2, dim=-1)
+            return diss.permute([1, 0, 2]).squeeze(-1)
+
+
 # Aliases
 sed = squared_euclidean_distance

prototorch/functions/helper.py

@@ -0,0 +1,89 @@
+import torch
+
+
+def calculate_prototype_accuracy(y_pred, y_true, plabels):
+    """Computes the accuracy of a prototype based model.
+    via Winner-Takes-All rule.
+    Requirement:
+    y_pred.shape == y_true.shape
+    unique(y_pred) in plabels
+    """
+    with torch.no_grad():
+        idx = torch.argmin(y_pred, axis=1)
+        return torch.true_divide(torch.sum(y_true == plabels[idx]),
+                                 len(y_pred)) * 100
+
+
+def predict_label(y_pred, plabels):
+    r""" Predicts labels given a prediction of a prototype based model.
+    """
+    with torch.no_grad():
+        return plabels[torch.argmin(y_pred, 1)]
+
+
+def mixed_shape(inputs):
+    if not torch.is_tensor(inputs):
+        raise ValueError('Input must be a tensor.')
+    else:
+        int_shape = list(inputs.shape)
+        # sometimes int_shape returns mixed integer types
+        int_shape = [int(i) if i is not None else i for i in int_shape]
+        tensor_shape = inputs.shape
+
+        for i, s in enumerate(int_shape):
+            if s is None:
+                int_shape[i] = tensor_shape[i]
+        return tuple(int_shape)
+
+
+def equal_int_shape(shape_1, shape_2):
+    if not isinstance(shape_1,
+                      (tuple, list)) or not isinstance(shape_2, (tuple, list)):
+        raise ValueError('Input shapes must list or tuple.')
+    for shape in [shape_1, shape_2]:
+        if not all([isinstance(x, int) or x is None for x in shape]):
+            raise ValueError(
+                'Input shapes must be list or tuple of int and None values.')
+
+    if len(shape_1) != len(shape_2):
+        return False
+    else:
+        for axis, value in enumerate(shape_1):
+            if value is not None and shape_2[axis] not in {value, None}:
+                return False
+        return True
+
+
+def _check_shapes(signal_int_shape, proto_int_shape):
+    if len(signal_int_shape) < 4:
+        raise ValueError(
+            "The number of signal dimensions must be >=4. You provide: " +
+            str(len(signal_int_shape)))
+
+    if len(proto_int_shape) < 2:
+        raise ValueError(
+            "The number of proto dimensions must be >=2. You provide: " +
+            str(len(proto_int_shape)))
+
+    if not equal_int_shape(signal_int_shape[3:], proto_int_shape[1:]):
+        raise ValueError(
+            "The atom shape of signals must be equal protos. You provide: signals.shape[3:]="
+            + str(signal_int_shape[3:]) + " != protos.shape[1:]=" +
+            str(proto_int_shape[1:]))
+
+    # not a sparse signal
+    if signal_int_shape[1] != 1:
+        if not equal_int_shape(signal_int_shape[1:2], proto_int_shape[0:1]):
+            raise ValueError(
+                "If the signal is not sparse, the number of prototypes must be equal in signals and "
+                "protos. You provide: " + str(signal_int_shape[1]) + " != " +
+                str(proto_int_shape[0]))
+
+    return True
+
+
+def _int_and_mixed_shape(tensor):
+    shape = mixed_shape(tensor)
+    int_shape = tuple([i if isinstance(i, int) else None for i in shape])
+
+    return shape, int_shape

prototorch/functions/normalization.py

@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import division
+
+import torch
+
+
+def orthogonalization(tensors):
+    r""" Orthogonalization of a given tensor via polar decomposition.
+    """
+    u, _, v = torch.svd(tensors, compute_uv=True)
+    u_shape = tuple(list(u.shape))
+    v_shape = tuple(list(v.shape))
+
+    # reshape to (num x N x M)
+    u = torch.reshape(u, (-1, u_shape[-2], u_shape[-1]))
+    v = torch.reshape(v, (-1, v_shape[-2], v_shape[-1]))
+
+    out = u @ v.permute([0, 2, 1])
+
+    out = torch.reshape(out, u_shape[:-1] + (v_shape[-2], ))
+
+    return out
+
+
+def trace_normalization(tensors):
+    r""" Trace normalization
+    """
+    epsilon = torch.tensor([1e-10], dtype=torch.float64)
+    # Scope trace_normalization
+    constant = torch.trace(tensors)
+
+    if epsilon != 0:
+        constant = torch.max(constant, epsilon)
+
+    return tensors / constant

prototorch/modules/models.py

@@ -0,0 +1,190 @@
+from torch import nn
+import torch
+from prototorch.modules.prototypes import Prototypes1D
+from prototorch.functions.distances import tangent_distance, euclidean_distance_matrix
+from prototorch.functions.normalization import orthogonalization
+from prototorch.functions.helper import _check_shapes, _int_and_mixed_shape
+
+
+class GTLVQ(nn.Module):
+    r""" Generalized Tangent Learning Vector Quantization
+
+    Parameters
+    ----------
+    num_classes: int
+        Number of classes of the given classification problem.
+
+    subspace_data: torch.tensor of shape (n_batch,feature_dim,feature_dim)
+        Subspace data for the point approximation, required
+
+    prototype_data: torch.tensor of shape (n_init_data,feature_dim) (optional)
+        prototype data for initalization of the prototypes used in GTLVQ.
+
+    subspace_size: int (default=256,optional)
+        Subspace dimension of the Projectors. Currently only supported
+        with tagnent_projection_type=global.
+
+    tangent_projection_type: string
+        Specifies the tangent projection type
+        options:    local
+                    local_proj
+                    global
+        local: computes the tangent distances without emphasizing projected
+        data. Only distances are available
+        local_proj: computs tangent distances and returns the projected data
+        for further use. Be careful: data is repeated by number of prototypes
+        global: Number of subspaces is set to one and every prototypes
+        uses the same.
+
+    prototypes_per_class: int (default=2,optional)
+    Number of prototypes per class
+
+    feature_dim: int (default=256)
+    Dimensionality of the feature space specified as integer.
+    Prototype dimension.
+
+    Notes
+    -----
+    The GTLVQ [1] is a prototype-based classification learning model. The
+    GTLVQ uses the Tangent-Distances for a local point approximation
+    of an assumed data manifold via prototypial representations.
+
+    The GTLVQ requires subspace projectors for transforming the data
+    and prototypes into the affine subspace. Every prototype is
+    equipped with a specific subpspace and represents a point
+    approximation of the assumed manifold.
+
+    In practice prototypes and data are projected on this manifold
+    and pairwise euclidean distance computes.
+
+    References
+    ----------
+    .. [1] Saralajew, Sascha; Villmann, Thomas: Transfer learning
+    in classification based on manifolc. models and its relation
+    to tangent metric learning. In: 2017 International Joint
+    Conference on Neural Networks (IJCNN).
+    Bd. 2017-May : IEEE, 2017, S. 1756–1765
+    """
+    def __init__(
+        self,
+        num_classes,
+        subspace_data=None,
+        prototype_data=None,
+        subspace_size=256,
+        tangent_projection_type='local',
+        prototypes_per_class=2,
+        feature_dim=256,
+    ):
+        super(GTLVQ, self).__init__()
+
+        self.num_protos = num_classes * prototypes_per_class
+        self.subspace_size = feature_dim if subspace_size is None else subspace_size
+        self.feature_dim = feature_dim
+
+        if subspace_data is None:
+            raise ValueError('Init Data must be specified!')
+
+        self.tpt = tangent_projection_type
+        with torch.no_grad():
+            if self.tpt == 'local' or self.tpt == 'local_proj':
+                self.init_local_subspace(subspace_data)
+            elif self.tpt == 'global':
+                self.init_gobal_subspace(subspace_data, subspace_size)
+            else:
+                self.subspaces = None
+
+        # Hypothesis-Margin-Classifier
+        self.cls = Prototypes1D(input_dim=feature_dim,
+                                prototypes_per_class=prototypes_per_class,
+                                nclasses=num_classes,
+                                prototype_initializer='stratified_mean',
+                                data=prototype_data)
+
+    def forward(self, x):
+        # Tangent Projection
+        if self.tpt == 'local_proj':
+            x_conform = x.unsqueeze(1).repeat_interleave(self.num_protos,
+                                                         1).unsqueeze(2)
+            dis, proj_x = self.local_tangent_projection(x_conform)
+
+            proj_x = proj_x.reshape(x.shape[0] * self.num_protos,
+                                    self.feature_dim)
+            return proj_x, dis
+        elif self.tpt == "local":
+            x_conform = x.unsqueeze(1).repeat_interleave(self.num_protos,
+                                                         1).unsqueeze(2)
+            dis = tangent_distance(x_conform, self.cls.prototypes,
+                                   self.subspaces)
+        elif self.tpt == "gloabl":
+            dis = self.global_tangent_distances(x)
+        else:
+            dis = (x @ self.cls.prototypes.T) / (
+                torch.norm(x, dim=1, keepdim=True) @ torch.norm(
+                    self.cls.prototypes, dim=1, keepdim=True).T)
+        return dis
+
+    def init_gobal_subspace(self, data, num_subspaces):
+        _, _, v = torch.svd(data)
+        subspace = (torch.eye(v.shape[0]) - (v @ v.T)).T
+        subspaces = subspace[:, :num_subspaces]
+        self.subspaces = torch.nn.Parameter(
+            subspaces).clone().detach().requires_grad_(True)
+
+    def init_local_subspace(self, data):
+        _, _, v = torch.svd(data)
+        inital_projector = (torch.eye(v.shape[0]) - (v @ v.T)).T
+        subspaces = inital_projector.unsqueeze(0).repeat_interleave(
+            self.num_protos, 0)
+        self.subspaces = torch.nn.Parameter(
+            subspaces).clone().detach().requires_grad_(True)
+
+    def global_tangent_distances(self, x):
+        # Tangent Projection
+        x, projected_prototypes = x @ self.subspaces, self.cls.prototypes @ self.subspaces
+        # Euclidean Distance
+        return euclidean_distance_matrix(x, projected_prototypes)
+
+    def local_tangent_projection(self,
+                                 signals):
+        # Note: subspaces is always assumed as transposed and must be orthogonal!
+        # shape(signals): batch x proto_number x channels x dim1 x dim2 x ... x dimN
+        # shape(protos): proto_number x dim1 x dim2 x ... x dimN
+        # shape(subspaces): (optional [proto_number]) x prod(dim1 * dim2 * ... * dimN)  x prod(projected_atom_shape)
+        # subspace should be orthogonalized
+        # Origin Source Code
+        # Origin Author:
+        protos = self.cls.prototypes
+        subspaces = self.subspaces
+        signal_shape, signal_int_shape = _int_and_mixed_shape(signals)
+        _, proto_int_shape = _int_and_mixed_shape(protos)
+
+        # check if the shapes are correct
+        _check_shapes(signal_int_shape, proto_int_shape)
+
+        # Tangent Data Projections
+        projected_protos = torch.bmm(protos.unsqueeze(1), subspaces).squeeze(1)
+        data = signals.squeeze(2).permute([1, 0, 2])
+        projected_data = torch.bmm(data, subspaces)
+        projected_data = projected_data.permute([1, 0, 2]).unsqueeze(1)
+        diff = projected_data - projected_protos
+        projected_diff = torch.reshape(
+            diff, (signal_shape[1], signal_shape[0], signal_shape[2]) +
+            signal_shape[3:])
+        diss = torch.norm(projected_diff, 2, dim=-1)
+        return diss.permute([1, 0, 2]).squeeze(-1), projected_data.squeeze(1)
+
+    def get_parameters(self):
+        return {
+            "params": self.cls.prototypes,
+        }, {
+            "params": self.subspaces
+        }
+
+    def orthogonalize_subspace(self):
+        if self.subspaces is not None:
+            with torch.no_grad():
+                ortho_subpsaces = orthogonalization(
+                    self.subspaces
+                ) if self.tpt == 'global' else torch.nn.init.orthogonal_(
+                    self.subspaces)
+                self.subspaces.copy_(ortho_subpsaces)

prototorch/modules/prototypes.py

@@ -14,55 +14,24 @@ class _Prototypes(torch.nn.Module):
 
     def _validate_prototype_distribution(self):
         if 0 in self.prototype_distribution:
-            warnings.warn('Are you sure about the `0` in '
-                          '`prototype_distribution`?')
+            warnings.warn("Are you sure about the `0` in "
+                          "`prototype_distribution`?")
 
     def extra_repr(self):
-        return f'prototypes.shape: {tuple(self.prototypes.shape)}'
+        return f"prototypes.shape: {tuple(self.prototypes.shape)}"
 
     def forward(self):
         return self.prototypes, self.prototype_labels
 
 
 class Prototypes1D(_Prototypes):
-    r"""Create a learnable set of one-dimensional prototypes.
+    """Create a learnable set of one-dimensional prototypes.
 
-    TODO Complete this doc-string
-
-    Kwargs:
-        prototypes_per_class: number of prototypes to use per class.
-            Default: ``1``
-        prototype_initializer: prototype initializer.
-            Default: ``'ones'``
-        prototype_distribution: prototype distribution vector.
-            Default: ``None``
-        input_dim: dimension of the incoming data.
-        nclasses: number of classes.
-        data: If set to ``None``, data-dependent initializers will be ignored.
-            Default: ``None``
-
-    Shape:
-        - Input: :math:`(N, H_{in})`
-            where :math:`H_{in} = \text{input_dim}`.
-        - Output: :math:`(N, H_{out})`
-            where :math:`H_{out} = \text{total_prototypes}`.
-
-    Attributes:
-        prototypes: the learnable weights of the module of shape
-            :math:`(\text{total_prototypes}, \text{prototype_dimension})`.
-        prototype_labels: the non-learnable labels of the prototypes.
-
-    Examples:
-
-        >>> p = Prototypes1D(input_dim=20, nclasses=10)
-        >>> input = torch.randn(128, 20)
-        >>> output = m(input)
-        >>> print(output.size())
-        torch.Size([20, 10])
+    TODO Complete this doc-string.
     """
     def __init__(self,
                  prototypes_per_class=1,
-                 prototype_initializer='ones',
+                 prototype_initializer="ones",
                  prototype_distribution=None,
                  data=None,
                  dtype=torch.float32,
@@ -75,25 +44,25 @@ class Prototypes1D(_Prototypes):
                 prototype_distribution = prototype_distribution.tolist()
 
         if data is None:
-            if 'input_dim' not in kwargs:
-                raise NameError('`input_dim` required if '
-                                'no `data` is provided.')
+            if "input_dim" not in kwargs:
+                raise NameError("`input_dim` required if "
+                                "no `data` is provided.")
             if prototype_distribution:
                 kwargs_nclasses = sum(prototype_distribution)
             else:
-                if 'nclasses' not in kwargs:
-                    raise NameError('`prototype_distribution` required if '
-                                    'both `data` and `nclasses` are not '
-                                    'provided.')
-                kwargs_nclasses = kwargs.pop('nclasses')
-            input_dim = kwargs.pop('input_dim')
+                if "nclasses" not in kwargs:
+                    raise NameError("`prototype_distribution` required if "
+                                    "both `data` and `nclasses` are not "
+                                    "provided.")
+                kwargs_nclasses = kwargs.pop("nclasses")
+            input_dim = kwargs.pop("input_dim")
             if prototype_initializer in [
-                    'stratified_mean', 'stratified_random'
+                    "stratified_mean", "stratified_random"
             ]:
                 warnings.warn(
-                    f'`prototype_initializer`: `{prototype_initializer}` '
-                    'requires `data`, but `data` is not provided. '
-                    'Using randomly generated data instead.')
+                    f"`prototype_initializer`: `{prototype_initializer}` "
+                    "requires `data`, but `data` is not provided. "
+                    "Using randomly generated data instead.")
             x_train = torch.rand(kwargs_nclasses, input_dim)
             y_train = torch.arange(kwargs_nclasses)
             if one_hot_labels:
@@ -106,39 +75,39 @@ class Prototypes1D(_Prototypes):
         nclasses = torch.unique(y_train, dim=-1).shape[-1]
 
         if nclasses == 1:
-            warnings.warn('Are you sure about having one class only?')
+            warnings.warn("Are you sure about having one class only?")
 
         if x_train.ndim != 2:
-            raise ValueError('`data[0].ndim != 2`.')
+            raise ValueError("`data[0].ndim != 2`.")
 
         if y_train.ndim == 2:
             if y_train.shape[1] == 1 and one_hot_labels:
-                raise ValueError('`one_hot_labels` is set to `True` '
-                                 'but target labels are not one-hot-encoded.')
+                raise ValueError("`one_hot_labels` is set to `True` "
+                                 "but target labels are not one-hot-encoded.")
             if y_train.shape[1] != 1 and not one_hot_labels:
-                raise ValueError('`one_hot_labels` is set to `False` '
-                                 'but target labels in `data` '
-                                 'are one-hot-encoded.')
+                raise ValueError("`one_hot_labels` is set to `False` "
+                                 "but target labels in `data` "
+                                 "are one-hot-encoded.")
         if y_train.ndim == 1 and one_hot_labels:
-            raise ValueError('`one_hot_labels` is set to `True` '
-                             'but target labels are not one-hot-encoded.')
+            raise ValueError("`one_hot_labels` is set to `True` "
+                             "but target labels are not one-hot-encoded.")
 
         # Verify input dimension if `input_dim` is provided
-        if 'input_dim' in kwargs:
-            input_dim = kwargs.pop('input_dim')
+        if "input_dim" in kwargs:
+            input_dim = kwargs.pop("input_dim")
             if input_dim != x_train.shape[1]:
-                raise ValueError(f'Provided `input_dim`={input_dim} does '
-                                 'not match data dimension '
-                                 f'`data[0].shape[1]`={x_train.shape[1]}')
+                raise ValueError(f"Provided `input_dim`={input_dim} does "
+                                 "not match data dimension "
+                                 f"`data[0].shape[1]`={x_train.shape[1]}")
 
         # Verify the number of classes if `nclasses` is provided
-        if 'nclasses' in kwargs:
-            kwargs_nclasses = kwargs.pop('nclasses')
+        if "nclasses" in kwargs:
+            kwargs_nclasses = kwargs.pop("nclasses")
             if kwargs_nclasses != nclasses:
-                raise ValueError(f'Provided `nclasses={kwargs_nclasses}` does '
-                                 'not match data labels '
-                                 '`torch.unique(data[1]).shape[0]`'
-                                 f'={nclasses}')
+                raise ValueError(f"Provided `nclasses={kwargs_nclasses}` does "
+                                 "not match data labels "
+                                 "`torch.unique(data[1]).shape[0]`"
+                                 f"={nclasses}")
 
         super().__init__(**kwargs)
 

setup.py

@@ -12,13 +12,6 @@ ProtoTorch Core Package
 from setuptools import setup
 from setuptools import find_packages
 
-from pkg_resources import safe_name
-
-import ast
-import importlib.util
-
-PKG_DIR = "prototorch"
-
 PROJECT_URL = "https://github.com/si-cim/prototorch"
 DOWNLOAD_URL = "https://github.com/si-cim/prototorch.git"
 
@@ -49,8 +42,8 @@ TESTS = ["pytest"]
 ALL = DOCS + DATASETS + EXAMPLES + TESTS
 
 setup(
-    name=safe_name(PKG_DIR),
-    use_scm_version=True,
+    name="prototorch",
+    version="0.2.0",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",
@@ -62,7 +55,6 @@ setup(
     download_url=DOWNLOAD_URL,
     license="MIT",
     install_requires=INSTALL_REQUIRES,
-    setup_requires=["setuptools_scm"],
     extras_require={
         "docs": DOCS,
         "datasets": DATASETS,