From 7c96050e20382fdd2312584dd0cf8ee091329181 Mon Sep 17 00:00:00 2001 From: Federico Aguzzi <62149513+f-aguzzi@users.noreply.github.com> Date: Tue, 4 Jun 2024 16:30:20 +0200 Subject: [PATCH] docs: new version --- docs/cookbook/structure.md | 173 +++++++++++++++--- .../case-study-classifier.md | 0 .../case-study-hybrid.md | 0 .../case-study-realtime.md | 0 .../introduction.md | 0 .../structure.md | 14 +- .../version-2.1.0/case-study-classifier.md | 9 + .../version-2.1.0/case-study-hybrid.md | 9 + .../version-2.1.0/case-study-realtime.md | 9 + .../version-2.1.0/introduction.md | 26 +++ .../version-2.1.0/structure.md | 44 +++++ ...ebars.json => version-2.0.0-sidebars.json} | 0 .../version-2.1.0-sidebars.json} | 0 docs/cookbook_versions.json | 3 +- docs/docs/lldf/lldfmodel.md | 1 + docs/docs/pca/pcadatamodel.md | 1 + docs/docusaurus.config.js | 15 +- .../complete-workflow.md | 0 .../knn/_category_.json | 0 .../{version-1.2 => version-1.2.0}/knn/knn.md | 0 .../knn/knnsettings.md | 0 .../lda/_category_.json | 0 .../{version-1.2 => version-1.2.0}/lda/lda.md | 0 .../lda/ldasettings.md | 0 .../lldf/_category_.json | 0 .../lldf/index.mdx | 0 .../lldf/lldf-class.md | 0 .../lldf/lldfmodel.md | 0 .../lldf/lldfsettings.md | 0 .../lldf/table.md | 0 .../lr/_category_.json | 0 .../{version-1.2 => version-1.2.0}/lr/lr.md | 0 .../lr/lrsettings.md | 0 .../pca/_category_.json | 0 .../{version-1.2 => version-1.2.0}/pca/pca.md | 0 .../pca/pcasettings.md | 0 .../plsda/_category_.json | 0 .../plsda/plsda.md | 0 .../plsda/plsdasettings.md | 0 .../svm/_category_.json | 0 .../{version-1.2 => version-1.2.0}/svm/svm.md | 0 .../svm/svmsettings.md | 0 .../tutorial.md | 0 .../utils/_category_.json | 0 .../utils/graphmode.md | 0 .../utils/graphoutput.md | 0 .../utils/printconfusionmatrix.md | 0 .../utils/printtable.md | 0 .../utils/runsplittests.md | 0 .../base/_category_.json | 0 .../base/baseclassifier.md | 0 .../base/basedatamodel.md | 0 .../base/basesettings.md | 0 .../complete-workflow.md | 0 .../knn/_category_.json | 0 .../{version-2.0 => version-2.0.0}/knn/knn.md | 0 .../knn/knnsettings.md | 0 .../lda/_category_.json | 0 .../{version-2.0 => version-2.0.0}/lda/lda.md | 0 .../lda/ldasettings.md | 0 .../lldf/_category_.json | 0 .../lldf/index.mdx | 0 .../lldf/lldf-class.md | 0 .../lldf/lldfmodel.md | 0 .../lldf/lldfsettings.md | 0 .../lldf/table.md | 0 .../lr/_category_.json | 0 .../{version-2.0 => version-2.0.0}/lr/lr.md | 0 .../lr/lrsettings.md | 0 .../pca/_category_.json | 0 .../{version-2.0 => version-2.0.0}/pca/pca.md | 0 .../pca/pcasettings.md | 0 .../plsda/_category_.json | 0 .../plsda/plsda.md | 0 .../plsda/plsdasettings.md | 0 .../svm/_category_.json | 0 .../{version-2.0 => version-2.0.0}/svm/svm.md | 0 .../svm/svmsettings.md | 0 .../tutorial.md | 0 .../utils/_category_.json | 0 .../utils/graphmode.md | 0 .../utils/graphoutput.md | 0 .../utils/printconfusionmatrix.md | 0 .../utils/printtable.md | 0 .../utils/runsplittests.md | 0 .../version-2.1.0/base/_category_.json | 8 + .../version-2.1.0/base/baseclassifier.md | 33 ++++ .../version-2.1.0/base/basedatamodel.md | 21 +++ .../version-2.1.0/base/basesettings.md | 21 +++ .../version-2.1.0/complete-workflow.md | 31 ++++ .../version-2.1.0/knn/_category_.json | 8 + docs/versioned_docs/version-2.1.0/knn/knn.md | 47 +++++ .../version-2.1.0/knn/knnsettings.md | 64 +++++++ .../version-2.1.0/lda/_category_.json | 8 + docs/versioned_docs/version-2.1.0/lda/lda.md | 48 +++++ .../version-2.1.0/lda/ldasettings.md | 39 ++++ .../version-2.1.0/lldf/_category_.json | 8 + .../version-2.1.0/lldf/index.mdx | 47 +++++ .../version-2.1.0/lldf/lldf-class.md | 67 +++++++ .../version-2.1.0/lldf/lldfmodel.md | 25 +++ .../version-2.1.0/lldf/lldfsettings.md | 25 +++ .../version-2.1.0/lldf/table.md | 39 ++++ .../version-2.1.0/lr/_category_.json | 8 + docs/versioned_docs/version-2.1.0/lr/lr.md | 51 ++++++ .../version-2.1.0/lr/lrsettings.md | 44 +++++ .../version-2.1.0/pca/_category_.json | 8 + docs/versioned_docs/version-2.1.0/pca/pca.md | 46 +++++ .../version-2.1.0/pca/pcadatamodel.md | 25 +++ .../version-2.1.0/pca/pcasettings.md | 41 +++++ .../version-2.1.0/plsda/_category_.json | 8 + .../version-2.1.0/plsda/plsda.md | 47 +++++ .../version-2.1.0/plsda/plsdasettings.md | 38 ++++ .../version-2.1.0/svm/_category_.json | 8 + docs/versioned_docs/version-2.1.0/svm/svm.md | 49 +++++ .../version-2.1.0/svm/svmsettings.md | 43 +++++ docs/versioned_docs/version-2.1.0/tutorial.md | 109 +++++++++++ .../version-2.1.0/utils/_category_.json | 8 + .../version-2.1.0/utils/graphmode.md | 11 ++ .../version-2.1.0/utils/graphoutput.md | 20 ++ .../utils/printconfusionmatrix.md | 19 ++ .../version-2.1.0/utils/printtable.md | 20 ++ .../version-2.1.0/utils/runsplittests.md | 20 ++ ...ebars.json => version-1.2.0-sidebars.json} | 0 .../version-2.0.0-sidebars.json | 8 + .../version-2.1.0-sidebars.json | 8 + docs/versions.json | 5 +- 126 files changed, 1437 insertions(+), 50 deletions(-) rename docs/cookbook_versioned_docs/{version-2.0 => version-2.0.0}/case-study-classifier.md (100%) rename docs/cookbook_versioned_docs/{version-2.0 => version-2.0.0}/case-study-hybrid.md (100%) rename docs/cookbook_versioned_docs/{version-2.0 => version-2.0.0}/case-study-realtime.md (100%) rename docs/cookbook_versioned_docs/{version-2.0 => version-2.0.0}/introduction.md (100%) rename docs/cookbook_versioned_docs/{version-2.0 => version-2.0.0}/structure.md (85%) create mode 100644 docs/cookbook_versioned_docs/version-2.1.0/case-study-classifier.md create mode 100644 docs/cookbook_versioned_docs/version-2.1.0/case-study-hybrid.md create mode 100644 docs/cookbook_versioned_docs/version-2.1.0/case-study-realtime.md create mode 100644 docs/cookbook_versioned_docs/version-2.1.0/introduction.md create mode 100644 docs/cookbook_versioned_docs/version-2.1.0/structure.md rename docs/cookbook_versioned_sidebars/{version-2.0-sidebars.json => version-2.0.0-sidebars.json} (100%) rename docs/{versioned_sidebars/version-1.2-sidebars.json => cookbook_versioned_sidebars/version-2.1.0-sidebars.json} (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/complete-workflow.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/knn/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/knn/knn.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/knn/knnsettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lda/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lda/lda.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lda/ldasettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/index.mdx (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/lldf-class.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/lldfmodel.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/lldfsettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lldf/table.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lr/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lr/lr.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/lr/lrsettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/pca/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/pca/pca.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/pca/pcasettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/plsda/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/plsda/plsda.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/plsda/plsdasettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/svm/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/svm/svm.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/svm/svmsettings.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/tutorial.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/_category_.json (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/graphmode.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/graphoutput.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/printconfusionmatrix.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/printtable.md (100%) rename docs/versioned_docs/{version-1.2 => version-1.2.0}/utils/runsplittests.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/base/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/base/baseclassifier.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/base/basedatamodel.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/base/basesettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/complete-workflow.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/knn/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/knn/knn.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/knn/knnsettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lda/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lda/lda.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lda/ldasettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/index.mdx (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/lldf-class.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/lldfmodel.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/lldfsettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lldf/table.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lr/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lr/lr.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/lr/lrsettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/pca/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/pca/pca.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/pca/pcasettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/plsda/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/plsda/plsda.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/plsda/plsdasettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/svm/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/svm/svm.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/svm/svmsettings.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/tutorial.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/_category_.json (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/graphmode.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/graphoutput.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/printconfusionmatrix.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/printtable.md (100%) rename docs/versioned_docs/{version-2.0 => version-2.0.0}/utils/runsplittests.md (100%) create mode 100644 docs/versioned_docs/version-2.1.0/base/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/base/baseclassifier.md create mode 100644 docs/versioned_docs/version-2.1.0/base/basedatamodel.md create mode 100644 docs/versioned_docs/version-2.1.0/base/basesettings.md create mode 100644 docs/versioned_docs/version-2.1.0/complete-workflow.md create mode 100644 docs/versioned_docs/version-2.1.0/knn/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/knn/knn.md create mode 100644 docs/versioned_docs/version-2.1.0/knn/knnsettings.md create mode 100644 docs/versioned_docs/version-2.1.0/lda/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/lda/lda.md create mode 100644 docs/versioned_docs/version-2.1.0/lda/ldasettings.md create mode 100644 docs/versioned_docs/version-2.1.0/lldf/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/lldf/index.mdx create mode 100644 docs/versioned_docs/version-2.1.0/lldf/lldf-class.md create mode 100644 docs/versioned_docs/version-2.1.0/lldf/lldfmodel.md create mode 100644 docs/versioned_docs/version-2.1.0/lldf/lldfsettings.md create mode 100644 docs/versioned_docs/version-2.1.0/lldf/table.md create mode 100644 docs/versioned_docs/version-2.1.0/lr/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/lr/lr.md create mode 100644 docs/versioned_docs/version-2.1.0/lr/lrsettings.md create mode 100644 docs/versioned_docs/version-2.1.0/pca/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/pca/pca.md create mode 100644 docs/versioned_docs/version-2.1.0/pca/pcadatamodel.md create mode 100644 docs/versioned_docs/version-2.1.0/pca/pcasettings.md create mode 100644 docs/versioned_docs/version-2.1.0/plsda/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/plsda/plsda.md create mode 100644 docs/versioned_docs/version-2.1.0/plsda/plsdasettings.md create mode 100644 docs/versioned_docs/version-2.1.0/svm/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/svm/svm.md create mode 100644 docs/versioned_docs/version-2.1.0/svm/svmsettings.md create mode 100644 docs/versioned_docs/version-2.1.0/tutorial.md create mode 100644 docs/versioned_docs/version-2.1.0/utils/_category_.json create mode 100644 docs/versioned_docs/version-2.1.0/utils/graphmode.md create mode 100644 docs/versioned_docs/version-2.1.0/utils/graphoutput.md create mode 100644 docs/versioned_docs/version-2.1.0/utils/printconfusionmatrix.md create mode 100644 docs/versioned_docs/version-2.1.0/utils/printtable.md create mode 100644 docs/versioned_docs/version-2.1.0/utils/runsplittests.md rename docs/versioned_sidebars/{version-2.0-sidebars.json => version-1.2.0-sidebars.json} (100%) create mode 100644 docs/versioned_sidebars/version-2.0.0-sidebars.json create mode 100644 docs/versioned_sidebars/version-2.1.0-sidebars.json diff --git a/docs/cookbook/structure.md b/docs/cookbook/structure.md index a1ec5d5..3850237 100644 --- a/docs/cookbook/structure.md +++ b/docs/cookbook/structure.md @@ -10,35 +10,148 @@ In this cookbook page, you will be shown how the project is structured, and the ``` chemfusekit - | - |＿lda - | |＿LDASettings - | |＿LDA - | - |＿lr - | |＿LRSettings - | |＿LR - | - |＿plsda - | |＿PLSDASettings - | |＿PLSDA - | - |＿pca - | |＿PCASettings - | |＿PCA - | - |＿lldf - | |＿LLDFSettings - | |＿LLDF - | |＿LLDFModel - | - |＿svm - | |＿SVMSettings - | |＿SVM - | - |＿knn - |＿KNNSettings - |＿KNN + │ + ├── lda + │ ├── LDASettings + │ └── LDA + │ + ├── lr + │ ├── LRSettings + │ └── LR + │ + ├── plsda + │ ├── PLSDASettings + │ └── PLSDA + │ + ├── pca + │ ├── PCASettings + │ ├── PCA + │ └── PCADataModel + │ + ├── lldf + │ ├── LLDFSettings + │ ├── LLDF + │ └── LLDFDataModel + │ + ├── svm + │ ├── SVMSettings + │ └── SVM + │ + └── knn + ├── KNNSettings + └── KNN ``` -As you can see, each module contains a class with the same name of the module, and a settings class. That's because this project tries to be as modular and as regular as possible, for clarity and interoperability. \ No newline at end of file +As you can see, each module contains a class with the same name of the module, and a settings class. That's because this project tries to be as modular and as regular as possible, for clarity and interoperability. + + +## Modular design features + +The settings for all classifiers (that is, all classes except `LLDF` and `PCA`) inherit from a base class called [`BaseSettings`](/docs/base/basesettings) in the `base` module: + +```mermaid +classDiagram + class BaseSettings { + +output: GraphMode + +test_split: bool + __init__(output, test_split) + } + + class KNNSettings { + ... + } + + class LDASettings { + ... + } + + class LRSettings { + ... + } + + class PLSDASettings { + ... + } + + class SVMSettings { + ... + } + + BaseSettings *-- KNNSettings + BaseSettings *-- LDASettings + BaseSettings *-- LRSettings + BaseSettings *-- PLSDASettings + BaseSettings *-- SVMSettings +``` + +\ +\ +The classifiers themselves all inherit from a base class called [`BaseClassifier`](/docs/base/baseclassifier) in the `base` module: + +```mermaid +classDiagram + + class BaseClassifier { + +settings: BaseSettings + +data: BaseDataModel + +model: sklearn model + __init__(settings, data) + import_model(import_path: str) + export_model(export_path: str) + } + + class KNN { + ... + } + + class LDA { + ... + } + + class LR { + ... + } + + class PLSDA { + ... + } + + class SVM { + ... + } + + BaseClassifier *-- KNN + BaseClassifier *-- LDA + BaseClassifier *-- LR + BaseClassifier *-- PLSDA + BaseClassifier *-- SVM +``` + +\ +\ +The data types are modular and interexchangeable too. Both [`LLDFDataModel`](/docs/lldf/lldfdatamodel) and [`PCADataModel`](/docs/pca/pcadatamodel) inherit from [`BaseDataModel`](/docs/base/basedatamodel) as shown in the following diagram: + +```mermaid +classDiagram + class BaseDataModel { + +x_data: DataFrame + +x_train: DataFrame + +y: ndarray + __init__(x_data, x_train, y) + } + + class LLDFDataModel { + ... + __init__(...) + } + + class PCADataModel { + +array_scores: ndarray + __init__(..., array_scores) + } + + BaseDataModel *-- LLDFDataModel + BaseDataModel *-- PCADataModel +``` + +This allows all the classifiers to use the `LLDF` data, dimension-reduced `PCA` data, or any other type of data as long as it follows the `BaseDataModel` template. \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.0/case-study-classifier.md b/docs/cookbook_versioned_docs/version-2.0.0/case-study-classifier.md similarity index 100% rename from docs/cookbook_versioned_docs/version-2.0/case-study-classifier.md rename to docs/cookbook_versioned_docs/version-2.0.0/case-study-classifier.md diff --git a/docs/cookbook_versioned_docs/version-2.0/case-study-hybrid.md b/docs/cookbook_versioned_docs/version-2.0.0/case-study-hybrid.md similarity index 100% rename from docs/cookbook_versioned_docs/version-2.0/case-study-hybrid.md rename to docs/cookbook_versioned_docs/version-2.0.0/case-study-hybrid.md diff --git a/docs/cookbook_versioned_docs/version-2.0/case-study-realtime.md b/docs/cookbook_versioned_docs/version-2.0.0/case-study-realtime.md similarity index 100% rename from docs/cookbook_versioned_docs/version-2.0/case-study-realtime.md rename to docs/cookbook_versioned_docs/version-2.0.0/case-study-realtime.md diff --git a/docs/cookbook_versioned_docs/version-2.0/introduction.md b/docs/cookbook_versioned_docs/version-2.0.0/introduction.md similarity index 100% rename from docs/cookbook_versioned_docs/version-2.0/introduction.md rename to docs/cookbook_versioned_docs/version-2.0.0/introduction.md diff --git a/docs/cookbook_versioned_docs/version-2.0/structure.md b/docs/cookbook_versioned_docs/version-2.0.0/structure.md similarity index 85% rename from docs/cookbook_versioned_docs/version-2.0/structure.md rename to docs/cookbook_versioned_docs/version-2.0.0/structure.md index 3850237..e9b28c0 100644 --- a/docs/cookbook_versioned_docs/version-2.0/structure.md +++ b/docs/cookbook_versioned_docs/version-2.0.0/structure.md @@ -86,7 +86,7 @@ classDiagram \ \ -The classifiers themselves all inherit from a base class called [`BaseClassifier`](/docs/base/baseclassifier) in the `base` module: +The classifiers themselves, except `LR`, all inherit from a base class called [`BaseClassifier`](/docs/base/baseclassifier) in the `base` module: ```mermaid classDiagram @@ -108,10 +108,6 @@ classDiagram ... } - class LR { - ... - } - class PLSDA { ... } @@ -145,13 +141,7 @@ classDiagram __init__(...) } - class PCADataModel { - +array_scores: ndarray - __init__(..., array_scores) - } - BaseDataModel *-- LLDFDataModel - BaseDataModel *-- PCADataModel ``` -This allows all the classifiers to use the `LLDF` data, dimension-reduced `PCA` data, or any other type of data as long as it follows the `BaseDataModel` template. \ No newline at end of file +This allows all the classifiers to use the `LLDF` data, or any other type of data as long as it follows the `BaseDataModel` template. \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.1.0/case-study-classifier.md b/docs/cookbook_versioned_docs/version-2.1.0/case-study-classifier.md new file mode 100644 index 0000000..8b1d3d3 --- /dev/null +++ b/docs/cookbook_versioned_docs/version-2.1.0/case-study-classifier.md @@ -0,0 +1,9 @@ +--- +sidebar_position: 3 +--- + +# Case study: training a classifier from lab data + +:::note +This case study is still **under construction**. +::: \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.1.0/case-study-hybrid.md b/docs/cookbook_versioned_docs/version-2.1.0/case-study-hybrid.md new file mode 100644 index 0000000..a7c4c5d --- /dev/null +++ b/docs/cookbook_versioned_docs/version-2.1.0/case-study-hybrid.md @@ -0,0 +1,9 @@ +--- +sidebar_position: 4 +--- + +# Case study: hybrid workflow + +:::note +This case study is still **under construction**. +::: \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.1.0/case-study-realtime.md b/docs/cookbook_versioned_docs/version-2.1.0/case-study-realtime.md new file mode 100644 index 0000000..8725eac --- /dev/null +++ b/docs/cookbook_versioned_docs/version-2.1.0/case-study-realtime.md @@ -0,0 +1,9 @@ +--- +sidebar_position: 5 +--- + +# Case study: real-time data classification + +:::note +This case study is still **under construction**. +::: \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.1.0/introduction.md b/docs/cookbook_versioned_docs/version-2.1.0/introduction.md new file mode 100644 index 0000000..3a4d2ef --- /dev/null +++ b/docs/cookbook_versioned_docs/version-2.1.0/introduction.md @@ -0,0 +1,26 @@ +--- +sidebar_position: 1 +--- + +# The ChemFuseKit Cookbook: an introduction + +*What is a cookbook, exactly?* + +> A cookbook is a comprehensive collection of recipes that guide users through +the process of learning and mastering the use of a specific library or +programming technique, by providing step-by-step instructions, explanations and +examples. + +## What you'll learn + +In this cookbook you will learn the basic principles of operation of `ChemFuseKit` through practical examples and case studies. You will be shown that all modules follow a basic structure, and once you've learned it for one module, you will be able to reapply that knowledge for all modules. + +You will be shown how to use the library on its own, and also how to use it as a part of a bigger pipeline. + +## Cookbook sectioning + +Here we go: + +- first of all, you will be shown the basic principles and structure; +- then, you will be shown three case studies; +- finally, you'll receive instructions on how to modify and expand this library for your own purposes. \ No newline at end of file diff --git a/docs/cookbook_versioned_docs/version-2.1.0/structure.md b/docs/cookbook_versioned_docs/version-2.1.0/structure.md new file mode 100644 index 0000000..a1ec5d5 --- /dev/null +++ b/docs/cookbook_versioned_docs/version-2.1.0/structure.md @@ -0,0 +1,44 @@ +--- +sidebar_position: 2 +--- + +# Project structure + +In this cookbook page, you will be shown how the project is structured, and the purpose of each module. + +## Project Hierarchy + +``` +chemfusekit + | + |＿lda + | |＿LDASettings + | |＿LDA + | + |＿lr + | |＿LRSettings + | |＿LR + | + |＿plsda + | |＿PLSDASettings + | |＿PLSDA + | + |＿pca + | |＿PCASettings + | |＿PCA + | + |＿lldf + | |＿LLDFSettings + | |＿LLDF + | |＿LLDFModel + | + |＿svm + | |＿SVMSettings + | |＿SVM + | + |＿knn + |＿KNNSettings + |＿KNN +``` + +As you can see, each module contains a class with the same name of the module, and a settings class. That's because this project tries to be as modular and as regular as possible, for clarity and interoperability. \ No newline at end of file diff --git a/docs/cookbook_versioned_sidebars/version-2.0-sidebars.json b/docs/cookbook_versioned_sidebars/version-2.0.0-sidebars.json similarity index 100% rename from docs/cookbook_versioned_sidebars/version-2.0-sidebars.json rename to docs/cookbook_versioned_sidebars/version-2.0.0-sidebars.json diff --git a/docs/versioned_sidebars/version-1.2-sidebars.json b/docs/cookbook_versioned_sidebars/version-2.1.0-sidebars.json similarity index 100% rename from docs/versioned_sidebars/version-1.2-sidebars.json rename to docs/cookbook_versioned_sidebars/version-2.1.0-sidebars.json diff --git a/docs/cookbook_versions.json b/docs/cookbook_versions.json index 59f17b2..dc236fe 100644 --- a/docs/cookbook_versions.json +++ b/docs/cookbook_versions.json @@ -1,3 +1,4 @@ [ - "2.0" + "2.1.0", + "2.0.0" ] diff --git a/docs/docs/lldf/lldfmodel.md b/docs/docs/lldf/lldfmodel.md index 859503a..7232264 100644 --- a/docs/docs/lldf/lldfmodel.md +++ b/docs/docs/lldf/lldfmodel.md @@ -19,6 +19,7 @@ LLDFModel(x_data: pd.DataFrame, x_train: pd.DataFrame, y: np.ndarray) The first two are `Pandas` `DataFrame` objects: - `x_data` - `x_train` + The last is a `NumPy` `ndarray`: - `y` diff --git a/docs/docs/pca/pcadatamodel.md b/docs/docs/pca/pcadatamodel.md index 00431c2..31cb3cb 100644 --- a/docs/docs/pca/pcadatamodel.md +++ b/docs/docs/pca/pcadatamodel.md @@ -19,6 +19,7 @@ PCAModel(x_data: pd.DataFrame, x_train: pd.DataFrame, y: np.ndarray, array_score The first two are `Pandas` `DataFrame` objects: - `x_data` - `x_train` + The last two are `NumPy` `ndarray`s: - `y` - `array_scores` diff --git a/docs/docusaurus.config.js b/docs/docusaurus.config.js index e5d4faa..a7ceace 100644 --- a/docs/docusaurus.config.js +++ b/docs/docusaurus.config.js @@ -101,11 +101,6 @@ const config = { label: 'Project', position: 'left', }, - { - to: 'blog', - label: 'Blog', - position: 'right' - }, { type: 'docSidebar', docsPluginId: 'cookbook', @@ -113,6 +108,16 @@ const config = { position: 'left', label: 'Cookbook', }, + { + type: 'docsVersionDropdown', + label: 'Docs version', + position: 'right' + }, + { + to: 'blog', + label: 'Blog', + position: 'right' + }, { href: 'https://github.com/f-aguzzi/tesi', label: 'GitHub', diff --git a/docs/versioned_docs/version-1.2/complete-workflow.md b/docs/versioned_docs/version-1.2.0/complete-workflow.md similarity index 100% rename from docs/versioned_docs/version-1.2/complete-workflow.md rename to docs/versioned_docs/version-1.2.0/complete-workflow.md diff --git a/docs/versioned_docs/version-1.2/knn/_category_.json b/docs/versioned_docs/version-1.2.0/knn/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/knn/_category_.json rename to docs/versioned_docs/version-1.2.0/knn/_category_.json diff --git a/docs/versioned_docs/version-1.2/knn/knn.md b/docs/versioned_docs/version-1.2.0/knn/knn.md similarity index 100% rename from docs/versioned_docs/version-1.2/knn/knn.md rename to docs/versioned_docs/version-1.2.0/knn/knn.md diff --git a/docs/versioned_docs/version-1.2/knn/knnsettings.md b/docs/versioned_docs/version-1.2.0/knn/knnsettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/knn/knnsettings.md rename to docs/versioned_docs/version-1.2.0/knn/knnsettings.md diff --git a/docs/versioned_docs/version-1.2/lda/_category_.json b/docs/versioned_docs/version-1.2.0/lda/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/lda/_category_.json rename to docs/versioned_docs/version-1.2.0/lda/_category_.json diff --git a/docs/versioned_docs/version-1.2/lda/lda.md b/docs/versioned_docs/version-1.2.0/lda/lda.md similarity index 100% rename from docs/versioned_docs/version-1.2/lda/lda.md rename to docs/versioned_docs/version-1.2.0/lda/lda.md diff --git a/docs/versioned_docs/version-1.2/lda/ldasettings.md b/docs/versioned_docs/version-1.2.0/lda/ldasettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/lda/ldasettings.md rename to docs/versioned_docs/version-1.2.0/lda/ldasettings.md diff --git a/docs/versioned_docs/version-1.2/lldf/_category_.json b/docs/versioned_docs/version-1.2.0/lldf/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/_category_.json rename to docs/versioned_docs/version-1.2.0/lldf/_category_.json diff --git a/docs/versioned_docs/version-1.2/lldf/index.mdx b/docs/versioned_docs/version-1.2.0/lldf/index.mdx similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/index.mdx rename to docs/versioned_docs/version-1.2.0/lldf/index.mdx diff --git a/docs/versioned_docs/version-1.2/lldf/lldf-class.md b/docs/versioned_docs/version-1.2.0/lldf/lldf-class.md similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/lldf-class.md rename to docs/versioned_docs/version-1.2.0/lldf/lldf-class.md diff --git a/docs/versioned_docs/version-1.2/lldf/lldfmodel.md b/docs/versioned_docs/version-1.2.0/lldf/lldfmodel.md similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/lldfmodel.md rename to docs/versioned_docs/version-1.2.0/lldf/lldfmodel.md diff --git a/docs/versioned_docs/version-1.2/lldf/lldfsettings.md b/docs/versioned_docs/version-1.2.0/lldf/lldfsettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/lldfsettings.md rename to docs/versioned_docs/version-1.2.0/lldf/lldfsettings.md diff --git a/docs/versioned_docs/version-1.2/lldf/table.md b/docs/versioned_docs/version-1.2.0/lldf/table.md similarity index 100% rename from docs/versioned_docs/version-1.2/lldf/table.md rename to docs/versioned_docs/version-1.2.0/lldf/table.md diff --git a/docs/versioned_docs/version-1.2/lr/_category_.json b/docs/versioned_docs/version-1.2.0/lr/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/lr/_category_.json rename to docs/versioned_docs/version-1.2.0/lr/_category_.json diff --git a/docs/versioned_docs/version-1.2/lr/lr.md b/docs/versioned_docs/version-1.2.0/lr/lr.md similarity index 100% rename from docs/versioned_docs/version-1.2/lr/lr.md rename to docs/versioned_docs/version-1.2.0/lr/lr.md diff --git a/docs/versioned_docs/version-1.2/lr/lrsettings.md b/docs/versioned_docs/version-1.2.0/lr/lrsettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/lr/lrsettings.md rename to docs/versioned_docs/version-1.2.0/lr/lrsettings.md diff --git a/docs/versioned_docs/version-1.2/pca/_category_.json b/docs/versioned_docs/version-1.2.0/pca/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/pca/_category_.json rename to docs/versioned_docs/version-1.2.0/pca/_category_.json diff --git a/docs/versioned_docs/version-1.2/pca/pca.md b/docs/versioned_docs/version-1.2.0/pca/pca.md similarity index 100% rename from docs/versioned_docs/version-1.2/pca/pca.md rename to docs/versioned_docs/version-1.2.0/pca/pca.md diff --git a/docs/versioned_docs/version-1.2/pca/pcasettings.md b/docs/versioned_docs/version-1.2.0/pca/pcasettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/pca/pcasettings.md rename to docs/versioned_docs/version-1.2.0/pca/pcasettings.md diff --git a/docs/versioned_docs/version-1.2/plsda/_category_.json b/docs/versioned_docs/version-1.2.0/plsda/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/plsda/_category_.json rename to docs/versioned_docs/version-1.2.0/plsda/_category_.json diff --git a/docs/versioned_docs/version-1.2/plsda/plsda.md b/docs/versioned_docs/version-1.2.0/plsda/plsda.md similarity index 100% rename from docs/versioned_docs/version-1.2/plsda/plsda.md rename to docs/versioned_docs/version-1.2.0/plsda/plsda.md diff --git a/docs/versioned_docs/version-1.2/plsda/plsdasettings.md b/docs/versioned_docs/version-1.2.0/plsda/plsdasettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/plsda/plsdasettings.md rename to docs/versioned_docs/version-1.2.0/plsda/plsdasettings.md diff --git a/docs/versioned_docs/version-1.2/svm/_category_.json b/docs/versioned_docs/version-1.2.0/svm/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/svm/_category_.json rename to docs/versioned_docs/version-1.2.0/svm/_category_.json diff --git a/docs/versioned_docs/version-1.2/svm/svm.md b/docs/versioned_docs/version-1.2.0/svm/svm.md similarity index 100% rename from docs/versioned_docs/version-1.2/svm/svm.md rename to docs/versioned_docs/version-1.2.0/svm/svm.md diff --git a/docs/versioned_docs/version-1.2/svm/svmsettings.md b/docs/versioned_docs/version-1.2.0/svm/svmsettings.md similarity index 100% rename from docs/versioned_docs/version-1.2/svm/svmsettings.md rename to docs/versioned_docs/version-1.2.0/svm/svmsettings.md diff --git a/docs/versioned_docs/version-1.2/tutorial.md b/docs/versioned_docs/version-1.2.0/tutorial.md similarity index 100% rename from docs/versioned_docs/version-1.2/tutorial.md rename to docs/versioned_docs/version-1.2.0/tutorial.md diff --git a/docs/versioned_docs/version-1.2/utils/_category_.json b/docs/versioned_docs/version-1.2.0/utils/_category_.json similarity index 100% rename from docs/versioned_docs/version-1.2/utils/_category_.json rename to docs/versioned_docs/version-1.2.0/utils/_category_.json diff --git a/docs/versioned_docs/version-1.2/utils/graphmode.md b/docs/versioned_docs/version-1.2.0/utils/graphmode.md similarity index 100% rename from docs/versioned_docs/version-1.2/utils/graphmode.md rename to docs/versioned_docs/version-1.2.0/utils/graphmode.md diff --git a/docs/versioned_docs/version-1.2/utils/graphoutput.md b/docs/versioned_docs/version-1.2.0/utils/graphoutput.md similarity index 100% rename from docs/versioned_docs/version-1.2/utils/graphoutput.md rename to docs/versioned_docs/version-1.2.0/utils/graphoutput.md diff --git a/docs/versioned_docs/version-1.2/utils/printconfusionmatrix.md b/docs/versioned_docs/version-1.2.0/utils/printconfusionmatrix.md similarity index 100% rename from docs/versioned_docs/version-1.2/utils/printconfusionmatrix.md rename to docs/versioned_docs/version-1.2.0/utils/printconfusionmatrix.md diff --git a/docs/versioned_docs/version-1.2/utils/printtable.md b/docs/versioned_docs/version-1.2.0/utils/printtable.md similarity index 100% rename from docs/versioned_docs/version-1.2/utils/printtable.md rename to docs/versioned_docs/version-1.2.0/utils/printtable.md diff --git a/docs/versioned_docs/version-1.2/utils/runsplittests.md b/docs/versioned_docs/version-1.2.0/utils/runsplittests.md similarity index 100% rename from docs/versioned_docs/version-1.2/utils/runsplittests.md rename to docs/versioned_docs/version-1.2.0/utils/runsplittests.md diff --git a/docs/versioned_docs/version-2.0/base/_category_.json b/docs/versioned_docs/version-2.0.0/base/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/base/_category_.json rename to docs/versioned_docs/version-2.0.0/base/_category_.json diff --git a/docs/versioned_docs/version-2.0/base/baseclassifier.md b/docs/versioned_docs/version-2.0.0/base/baseclassifier.md similarity index 100% rename from docs/versioned_docs/version-2.0/base/baseclassifier.md rename to docs/versioned_docs/version-2.0.0/base/baseclassifier.md diff --git a/docs/versioned_docs/version-2.0/base/basedatamodel.md b/docs/versioned_docs/version-2.0.0/base/basedatamodel.md similarity index 100% rename from docs/versioned_docs/version-2.0/base/basedatamodel.md rename to docs/versioned_docs/version-2.0.0/base/basedatamodel.md diff --git a/docs/versioned_docs/version-2.0/base/basesettings.md b/docs/versioned_docs/version-2.0.0/base/basesettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/base/basesettings.md rename to docs/versioned_docs/version-2.0.0/base/basesettings.md diff --git a/docs/versioned_docs/version-2.0/complete-workflow.md b/docs/versioned_docs/version-2.0.0/complete-workflow.md similarity index 100% rename from docs/versioned_docs/version-2.0/complete-workflow.md rename to docs/versioned_docs/version-2.0.0/complete-workflow.md diff --git a/docs/versioned_docs/version-2.0/knn/_category_.json b/docs/versioned_docs/version-2.0.0/knn/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/knn/_category_.json rename to docs/versioned_docs/version-2.0.0/knn/_category_.json diff --git a/docs/versioned_docs/version-2.0/knn/knn.md b/docs/versioned_docs/version-2.0.0/knn/knn.md similarity index 100% rename from docs/versioned_docs/version-2.0/knn/knn.md rename to docs/versioned_docs/version-2.0.0/knn/knn.md diff --git a/docs/versioned_docs/version-2.0/knn/knnsettings.md b/docs/versioned_docs/version-2.0.0/knn/knnsettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/knn/knnsettings.md rename to docs/versioned_docs/version-2.0.0/knn/knnsettings.md diff --git a/docs/versioned_docs/version-2.0/lda/_category_.json b/docs/versioned_docs/version-2.0.0/lda/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/lda/_category_.json rename to docs/versioned_docs/version-2.0.0/lda/_category_.json diff --git a/docs/versioned_docs/version-2.0/lda/lda.md b/docs/versioned_docs/version-2.0.0/lda/lda.md similarity index 100% rename from docs/versioned_docs/version-2.0/lda/lda.md rename to docs/versioned_docs/version-2.0.0/lda/lda.md diff --git a/docs/versioned_docs/version-2.0/lda/ldasettings.md b/docs/versioned_docs/version-2.0.0/lda/ldasettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/lda/ldasettings.md rename to docs/versioned_docs/version-2.0.0/lda/ldasettings.md diff --git a/docs/versioned_docs/version-2.0/lldf/_category_.json b/docs/versioned_docs/version-2.0.0/lldf/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/_category_.json rename to docs/versioned_docs/version-2.0.0/lldf/_category_.json diff --git a/docs/versioned_docs/version-2.0/lldf/index.mdx b/docs/versioned_docs/version-2.0.0/lldf/index.mdx similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/index.mdx rename to docs/versioned_docs/version-2.0.0/lldf/index.mdx diff --git a/docs/versioned_docs/version-2.0/lldf/lldf-class.md b/docs/versioned_docs/version-2.0.0/lldf/lldf-class.md similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/lldf-class.md rename to docs/versioned_docs/version-2.0.0/lldf/lldf-class.md diff --git a/docs/versioned_docs/version-2.0/lldf/lldfmodel.md b/docs/versioned_docs/version-2.0.0/lldf/lldfmodel.md similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/lldfmodel.md rename to docs/versioned_docs/version-2.0.0/lldf/lldfmodel.md diff --git a/docs/versioned_docs/version-2.0/lldf/lldfsettings.md b/docs/versioned_docs/version-2.0.0/lldf/lldfsettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/lldfsettings.md rename to docs/versioned_docs/version-2.0.0/lldf/lldfsettings.md diff --git a/docs/versioned_docs/version-2.0/lldf/table.md b/docs/versioned_docs/version-2.0.0/lldf/table.md similarity index 100% rename from docs/versioned_docs/version-2.0/lldf/table.md rename to docs/versioned_docs/version-2.0.0/lldf/table.md diff --git a/docs/versioned_docs/version-2.0/lr/_category_.json b/docs/versioned_docs/version-2.0.0/lr/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/lr/_category_.json rename to docs/versioned_docs/version-2.0.0/lr/_category_.json diff --git a/docs/versioned_docs/version-2.0/lr/lr.md b/docs/versioned_docs/version-2.0.0/lr/lr.md similarity index 100% rename from docs/versioned_docs/version-2.0/lr/lr.md rename to docs/versioned_docs/version-2.0.0/lr/lr.md diff --git a/docs/versioned_docs/version-2.0/lr/lrsettings.md b/docs/versioned_docs/version-2.0.0/lr/lrsettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/lr/lrsettings.md rename to docs/versioned_docs/version-2.0.0/lr/lrsettings.md diff --git a/docs/versioned_docs/version-2.0/pca/_category_.json b/docs/versioned_docs/version-2.0.0/pca/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/pca/_category_.json rename to docs/versioned_docs/version-2.0.0/pca/_category_.json diff --git a/docs/versioned_docs/version-2.0/pca/pca.md b/docs/versioned_docs/version-2.0.0/pca/pca.md similarity index 100% rename from docs/versioned_docs/version-2.0/pca/pca.md rename to docs/versioned_docs/version-2.0.0/pca/pca.md diff --git a/docs/versioned_docs/version-2.0/pca/pcasettings.md b/docs/versioned_docs/version-2.0.0/pca/pcasettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/pca/pcasettings.md rename to docs/versioned_docs/version-2.0.0/pca/pcasettings.md diff --git a/docs/versioned_docs/version-2.0/plsda/_category_.json b/docs/versioned_docs/version-2.0.0/plsda/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/plsda/_category_.json rename to docs/versioned_docs/version-2.0.0/plsda/_category_.json diff --git a/docs/versioned_docs/version-2.0/plsda/plsda.md b/docs/versioned_docs/version-2.0.0/plsda/plsda.md similarity index 100% rename from docs/versioned_docs/version-2.0/plsda/plsda.md rename to docs/versioned_docs/version-2.0.0/plsda/plsda.md diff --git a/docs/versioned_docs/version-2.0/plsda/plsdasettings.md b/docs/versioned_docs/version-2.0.0/plsda/plsdasettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/plsda/plsdasettings.md rename to docs/versioned_docs/version-2.0.0/plsda/plsdasettings.md diff --git a/docs/versioned_docs/version-2.0/svm/_category_.json b/docs/versioned_docs/version-2.0.0/svm/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/svm/_category_.json rename to docs/versioned_docs/version-2.0.0/svm/_category_.json diff --git a/docs/versioned_docs/version-2.0/svm/svm.md b/docs/versioned_docs/version-2.0.0/svm/svm.md similarity index 100% rename from docs/versioned_docs/version-2.0/svm/svm.md rename to docs/versioned_docs/version-2.0.0/svm/svm.md diff --git a/docs/versioned_docs/version-2.0/svm/svmsettings.md b/docs/versioned_docs/version-2.0.0/svm/svmsettings.md similarity index 100% rename from docs/versioned_docs/version-2.0/svm/svmsettings.md rename to docs/versioned_docs/version-2.0.0/svm/svmsettings.md diff --git a/docs/versioned_docs/version-2.0/tutorial.md b/docs/versioned_docs/version-2.0.0/tutorial.md similarity index 100% rename from docs/versioned_docs/version-2.0/tutorial.md rename to docs/versioned_docs/version-2.0.0/tutorial.md diff --git a/docs/versioned_docs/version-2.0/utils/_category_.json b/docs/versioned_docs/version-2.0.0/utils/_category_.json similarity index 100% rename from docs/versioned_docs/version-2.0/utils/_category_.json rename to docs/versioned_docs/version-2.0.0/utils/_category_.json diff --git a/docs/versioned_docs/version-2.0/utils/graphmode.md b/docs/versioned_docs/version-2.0.0/utils/graphmode.md similarity index 100% rename from docs/versioned_docs/version-2.0/utils/graphmode.md rename to docs/versioned_docs/version-2.0.0/utils/graphmode.md diff --git a/docs/versioned_docs/version-2.0/utils/graphoutput.md b/docs/versioned_docs/version-2.0.0/utils/graphoutput.md similarity index 100% rename from docs/versioned_docs/version-2.0/utils/graphoutput.md rename to docs/versioned_docs/version-2.0.0/utils/graphoutput.md diff --git a/docs/versioned_docs/version-2.0/utils/printconfusionmatrix.md b/docs/versioned_docs/version-2.0.0/utils/printconfusionmatrix.md similarity index 100% rename from docs/versioned_docs/version-2.0/utils/printconfusionmatrix.md rename to docs/versioned_docs/version-2.0.0/utils/printconfusionmatrix.md diff --git a/docs/versioned_docs/version-2.0/utils/printtable.md b/docs/versioned_docs/version-2.0.0/utils/printtable.md similarity index 100% rename from docs/versioned_docs/version-2.0/utils/printtable.md rename to docs/versioned_docs/version-2.0.0/utils/printtable.md diff --git a/docs/versioned_docs/version-2.0/utils/runsplittests.md b/docs/versioned_docs/version-2.0.0/utils/runsplittests.md similarity index 100% rename from docs/versioned_docs/version-2.0/utils/runsplittests.md rename to docs/versioned_docs/version-2.0.0/utils/runsplittests.md diff --git a/docs/versioned_docs/version-2.1.0/base/_category_.json b/docs/versioned_docs/version-2.1.0/base/_category_.json new file mode 100644 index 0000000..ac3f2d9 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/base/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "Base module", + "position": 9, + "link": { + "type": "generated-index", + "description": "A module containing base classes for all the other modules." + } +} diff --git a/docs/versioned_docs/version-2.1.0/base/baseclassifier.md b/docs/versioned_docs/version-2.1.0/base/baseclassifier.md new file mode 100644 index 0000000..9c80bcc --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/base/baseclassifier.md @@ -0,0 +1,33 @@ +--- +sidebar_position: 1 +--- + +# BaseClassifier class + +A base class from which all classifiers inherit. + +## Syntax + +```python +BaseClassifier(settings: BaseSettings, data: BaseDataModel) +``` + +## Constructor parameters + +- `settings`: object of type [`BaseSettings`](./basesettings.md). Contains the settings for + the `BaseClassifier` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +## Fields + +- `settings`: object of type [`KNNSettings`](/tesi/docs/knn/knnsettings). Contains the settings for + the `BaseClassifier` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. +- `model`: a `sklearn` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `import_model(import_path: str)`: loads a model from file +- `export_model(export_path: str)`: exports a model to file + - *raises*: + - `RuntimeError("You haven't trained the model yet! You cannot export it now.")` when trying to export an untrained model diff --git a/docs/versioned_docs/version-2.1.0/base/basedatamodel.md b/docs/versioned_docs/version-2.1.0/base/basedatamodel.md new file mode 100644 index 0000000..727c520 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/base/basedatamodel.md @@ -0,0 +1,21 @@ +--- +sidebar_position: 3 +--- + +# BaseDataModel class + +This class models the output data for all data-outputting operations (currently, the [`LLDF`](../lldf/lldf-class.md) operation and the [`PCA`](../pca/pca.md) operation). + +## Syntax + +```python +BaseDataModel(x_data: pd.DataFrame, x_train: pd.DataFrame, y: pd.DataFrame) +``` + +## Fields and constructor parameters + +The first two are `Pandas` `DataFrame` objects: +- `x_data` +- `x_train` +The last is a `NumPy` `ndarray`: +- `y` diff --git a/docs/versioned_docs/version-2.1.0/base/basesettings.md b/docs/versioned_docs/version-2.1.0/base/basesettings.md new file mode 100644 index 0000000..740581b --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/base/basesettings.md @@ -0,0 +1,21 @@ +--- +sidebar-position: 1 +--- + +# BaseSettings class + +Holds the settings for all classifier object. It's not meant for direct usage, only for inheritance. + + +## Syntax + +```python +BaseSettings(output: GraphMode, test_split: false) +``` + +## Fields and constructor parameters +- `output`: toggles graph output mode. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles the training split test phase. Defaults to `False`. Requires `output` to be set to `True` to work. + +The constructor raises: +- `Warning("You selected test_split but it won't run because you disabled the output.")` if `test_split` is run with `output` set to false (split tests only produce graphical output, and are useless when run with disabled output). diff --git a/docs/versioned_docs/version-2.1.0/complete-workflow.md b/docs/versioned_docs/version-2.1.0/complete-workflow.md new file mode 100644 index 0000000..f607520 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/complete-workflow.md @@ -0,0 +1,31 @@ +--- +sidebar-position: 7 +--- + +# Complete workflow + +Here's a sequence diagram to represent an example workflow, from the raw data +tables to classification, including data fusion, PCA and training. + +```plantuml +actor User +participant LLDF +participant PCA +participant Classifier + +User -> LLDF : Upload training tables +User -> LLDF : Set parameters +User -> Classifier : (optional) Upload model + +LLDF -> PCA : Pass preprocessed / fused tables +LLDF --> User : Download fused tables +LLDF -> Classifier : Pass preprocessed / fused tables \nRun classification +PCA -> Classifier : (optional) Set number of components + +Classifier --> User : classification results, graphs +PCA --> User : classification results, graphs +Classifier --> User : (optional) download trained model + +User -> Classifier : pass data to classify +Classifier --> User : classification results +``` diff --git a/docs/versioned_docs/version-2.1.0/knn/_category_.json b/docs/versioned_docs/version-2.1.0/knn/_category_.json new file mode 100644 index 0000000..e670264 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/knn/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "kNN module", + "position": 6, + "link": { + "type": "generated-index", + "description": "A module for k-nearest neighbors analysis." + } +} diff --git a/docs/versioned_docs/version-2.1.0/knn/knn.md b/docs/versioned_docs/version-2.1.0/knn/knn.md new file mode 100644 index 0000000..2cecad5 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/knn/knn.md @@ -0,0 +1,47 @@ +--- +sidebar_position: 1 +--- + +# KNN class + +A class to store the data, methods and artifacts for _k-Nearest Neighbors Analysis_. + +## Syntax + +```python +KNN(settings: KNNSettings, data: LLDFModel) +``` + +## Constructor parameters + +- `settings`: object of type [`KNNSettings`](knnsettings.md). Contains the settings for + the `KNN` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +## Fields + +- `settings`: object of type [`KNNSettings`](/tesi/docs/knn/knnsettings). Contains the settings for + the `KNN` object. +- `fused_data`: onject of type ['LLDFModel`](/tesi/docs/lldf/lldfmodel). Contains the + artifacts from the data fusion process. +- `model`: a `KNeighborsClassifier` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `knn(self)`: trains the k-Neighbors Analysis model +- `predict(self, x_data)`: performs LDA prediction once the model is trained. + - *raises*: + - `RuntimeError("The kNN model is not trained yet!")` if the `KNN` model hasn't been trained yet + +## Example + +```python +from chemfusekit.knn import KNN + +# Initialize and run the LDA class +knn = KNN(settings, lldf.fused_data) +knn.knn() + +# Run predictions +knn.predict(x_data) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/knn/knnsettings.md b/docs/versioned_docs/version-2.1.0/knn/knnsettings.md new file mode 100644 index 0000000..81f9486 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/knn/knnsettings.md @@ -0,0 +1,64 @@ +--- +sidebar-position: 1 +--- + +# KNNSettings class + +Holds the settings for the [`KNN`](knn.md) object. + +Inherits from [`BaseSettings`](../base/basesettings.md). + +## Syntax + +```python +KNNSettings( + n_neighbors: int, + metric: str | Callable, + weights: str | Callable, + algorithm: str, + output: GraphMode, + test_split: false +) +``` + +## Fields and constructor parameters +- `n_neighbors`: the amount of components to be used in the `KNN` model. Defaults to 15. +- `metric`: the distance metric for the model. It can take one of the following values: + - `minkwoski` + - `precomputed` + - `euclidean` + or be a callable object. +- `weights`: the weight metric for the model. It can take one of the following values: + - `uniform` + - `distance` + or be a callable object. +- `algorithm`: the algorithm for the model. It can take one of the following values: + - `auto` + - `ball_tree` + - `kd_tree` + - `brute` + or be a callable object. +- `output`: toggles graph output mode. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles the training split test phase. Defaults to `False`. Requires `output` to be set to `True` to work. + +The constructor raises: +- `ValueError("Invalid n_neighbors number: should be a positive integer.")` if the number of components is not valid. +- `ValueError("Invalid metric: should be 'minkwoski', 'precomputed', 'euclidean' or a callable.")` if the chosen metric is neither available nor a callable function. +- `ValueError("Invalid weight: should be 'uniform', 'distance' or a callable")` if the chosen weight is neither available nor a callable function. +- `ValueError("Invalid algorithm: should be 'auto', 'ball_tree', 'kd_tree' or 'brute'.")` if the chosen algotithm does not exist. +- `Warning("You selected test_split but it won't run because you disabled the output.")` if `test_split` is run with `output` set to false (split tests only produce graphical output, and are useless when run with disabled output). + +## Example + +```python +from chemfusekit.knn import KNNSettings, GraphMode + +settings = KNNSettings( + n_neighbors=20, # pick 20 neighbors + metric='minkowski', # choose the metric + weights='distance', # choose the weight metric + algorithm='auto', # the best algorithm gets chosen automatically + output=GraphMode.GRAPHIC, # graph output is enabled + test_split=True # the model will be split-tested at the end of the training +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lda/_category_.json b/docs/versioned_docs/version-2.1.0/lda/_category_.json new file mode 100644 index 0000000..8d1f6af --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lda/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "LDA module", + "position": 4, + "link": { + "type": "generated-index", + "description": "A module for linear discriminant analysis." + } +} diff --git a/docs/versioned_docs/version-2.1.0/lda/lda.md b/docs/versioned_docs/version-2.1.0/lda/lda.md new file mode 100644 index 0000000..2b8f19e --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lda/lda.md @@ -0,0 +1,48 @@ +--- +sidebar_position: 1 +--- + +# LDA class + +A class to store the data, methods and artifacts for _Linear Discriminant Analysis_. + +## Syntax + +```python +LDA(settings: LDASettings, data: BaseDataModel) +``` + +## Constructor parameters + +- `settings`: object of type [`LDASettings`](./ldasettings.md). Contains the settings for + the `LDA` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +## Fields + +- `settings`: object of type [`LDASettings`](./ldasettings.md). Contains the settings for + the `LDA` object. +- Fused data fields: + - `x_data` + - `x_train` + - `y` +- `model`: a `LinearDiscriminantAnalysis` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `lda(self)`: performs Linear Discriminant Analysis +- `__print_prediction_graphs(self, y_test, y_pred)`: helper function to print + graphs and stats about LDA predictions +- `predict(self, x_data)`: performs LDA prediction once the model is trained. + - *raises*: + - `RuntimeError("The LDA model is not trained yet!")` if the LDA model hasn't been trained yet + +## Example + +```python +from chemfusekit.lda import LDA + +# Initialize and run the LDA class +lda = LDA(lldf.fused_data, settings) +lda.lda() +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lda/ldasettings.md b/docs/versioned_docs/version-2.1.0/lda/ldasettings.md new file mode 100644 index 0000000..c9c850e --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lda/ldasettings.md @@ -0,0 +1,39 @@ +--- +sidebar_position: 2 +--- + +# LDASettings class + +Holds the settings for the [`LDA`](./lda.md) object. + +Inherits from [`BaseSettings`](../base/basesettings.md). + +## Syntax + +```python +LDASettings(components: int, output: GraphMode, split_test: bool) +``` + +## Fields and constructor parameters + +- `components`: the amount of components to be used in the LDA model. Defaults to 3. +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles split testing. Defaults to `False`. + + +The constructor raises: +- `ValueError("Invalid component number: must be a > 1 integer.")` if the number of + components is not valid. +- `Warning("You selected test_split but it won't run because you disabled the output.")` if split tests are run with `output` disabled + +## Example + +```python +from chemfusekit.lda import LDASettings, GraphMode + +settings = LDASettings( + components=(pca.components - 1), # one less component than the number determined by PCA + output=GraphMode.GRAPHIC, # graphs will be printed + test_split=True # split testing is enabled +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lldf/_category_.json b/docs/versioned_docs/version-2.1.0/lldf/_category_.json new file mode 100644 index 0000000..096ed0c --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "LLDF Module", + "position": 2, + "link": { + "type": "doc", + "id": "index" + } +} diff --git a/docs/versioned_docs/version-2.1.0/lldf/index.mdx b/docs/versioned_docs/version-2.1.0/lldf/index.mdx new file mode 100644 index 0000000..01c1d16 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/index.mdx @@ -0,0 +1,47 @@ +import DocCardList from '@theme/DocCardList'; + +# LLDF Module + +A module for low-level data fusion. + +# Members + + + +# UML + +```mermaid +classDiagram + class Table { + +str file_path + +str sheet_name + +str preprocessing + __init__(file_path, sheet_name, preprocessing) + } + + class LLDFSettings { + +GraphOutput output + __init__(output) + } + + class LLDF { + +LLDFSettings settings + +Table[] tables + +LLDFDataModel | None fused_data + lldf() + -_snv() + +export_data(export_path: str) + __init__(settings, tables[]) + } + + class LLDFDataModel { + +x_data: pd.DataFrame + +x_train: pd.DataFrame + +y: np.ndarray + __init__(x_data, x_train, y) + } + + LLDF *-- LLDFModel + LLDF *-- Table + LLDF *-- LLDFSettings +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lldf/lldf-class.md b/docs/versioned_docs/version-2.1.0/lldf/lldf-class.md new file mode 100644 index 0000000..1a0be38 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/lldf-class.md @@ -0,0 +1,67 @@ +--- +sidebar_position: 1 +--- + +# LLDF class + +The `LLDF` class is used for _low-level data fusion_. + +## Syntax + +```python +LLDF(tables: List[Table], lldf_settings: LLDFSettings) +``` + +## Constructor parameters + +- `tables`: `List[`[`Table`](./table.md)`]` + + A list of `Table` objects containing info about the files to import + +- `lldf_settings`: [`LLDFSettings`](./lldfsettings) + + The settings for the LLDF object. + +## Fields + +- `settings`: [`LLDFSettings`](./lldfsettings) + + The settings for the LLDF object. + +- `tables`: `List[`[`Table`](./table.md)`]` + + A list of `Table` objects containing info about the files to import + +- `fused_data`: [`LLDFModel`](./lldfmodel.md) + + The resulting model containing the data fusion artifacts. + +## Methods + +- `_snv(self, input_data)`: static method to rescale input arrays +- `lldf(self)`: performs low-level data fusion on the data passed in the settings + - *raises*: + - `FileNotFoundError("Error opening the selected files.")` + if the files specified in the settings are not valid + - `SyntaxError("LLDF: this type of preprocessing does not exist")` + if the preprocessing method specified in the settings is not valid +- `export_data(self, export_path)`: exports the data fusion artifacts to an Excel file + - *raises*: + - `RuntimeError("Cannot export data before data fusion.")` if export is + attempted before fusing the data + - `RuntimeError("Could not export data to the selected path.")` if any error + happens during the export phase + + +## Example + +```python +from chemfusekit.lldf import LLDF + +# Initialize and run low-level data fusion +lldf = LLDF(tables, lldf_settings) +lldf.lldf() + +# Export the LLDF data to an Excel file +lldf.export_data('output_file.xlsx') +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lldf/lldfmodel.md b/docs/versioned_docs/version-2.1.0/lldf/lldfmodel.md new file mode 100644 index 0000000..7232264 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/lldfmodel.md @@ -0,0 +1,25 @@ +--- +sidebar_position: 3 +--- + +# LLDFDataModel class + +This class models the output data from the [`LLDF`](./lldf-class.md) operation. + +It inherits from the [`BaseDataModel`](../base/basedatamodel.md). + +## Syntax + +```python +LLDFModel(x_data: pd.DataFrame, x_train: pd.DataFrame, y: np.ndarray) +``` + +## Fields and constructor parameters + +The first two are `Pandas` `DataFrame` objects: +- `x_data` +- `x_train` + +The last is a `NumPy` `ndarray`: +- `y` + diff --git a/docs/versioned_docs/version-2.1.0/lldf/lldfsettings.md b/docs/versioned_docs/version-2.1.0/lldf/lldfsettings.md new file mode 100644 index 0000000..30f985f --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/lldfsettings.md @@ -0,0 +1,25 @@ +--- +sidebar_position: 2 +--- + +# LLDFSettings class + +Holds the settings for the [`LLDF`](./lldf-class.md) object. + +## Syntax + +```python +LLDFSettings(output: GraphMode) +``` + +## Fields and constructor parameters +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). + +## Example + +```python +from chemfusekit.lldf import LLDFSettings + +# Initialize the settings for low-level data fusion +lldf_settings = LLDFSettings(output=GraphMode.TEXT) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lldf/table.md b/docs/versioned_docs/version-2.1.0/lldf/table.md new file mode 100644 index 0000000..782da64 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lldf/table.md @@ -0,0 +1,39 @@ +--- +sidebar_position: 4 +--- + +# Table class + +Holds the information for a single table to import. + +The [`LLDF`](./lldf-class.md) object takes a list of `Table` as a parameter. + +## Syntax + +```python +Table( + file_path: str + sheet_name: str + preprocessing: str +) +``` + +## Fields and constructor parameters + +- `file_path`: a `str` containing the path to the Excel datasheet +- `sheet_name`: a `str` containing the name of the sheet to select within the Excel file +- `preprocessing`: a `str` with the name of the preprocessing to be applied to the table. + Available options: `snv` (normalization), `savgol` (Savitski-Golay smoothing), `savgol+snv` (both), `none` (no processing). + +## Example + +```python +from chemfusekit.lldf import Table + +# Create a table +table1 = Table( + file_path='tests/qepas.xlsx', + sheet_name='Sheet1', + preprocessing='snv' # normalization preprocessing; other options: savgol, both or none +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lr/_category_.json b/docs/versioned_docs/version-2.1.0/lr/_category_.json new file mode 100644 index 0000000..c9a9071 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lr/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "LR module", + "position": 6, + "link": { + "type": "generated-index", + "description": "A module for logistic regression." + } +} diff --git a/docs/versioned_docs/version-2.1.0/lr/lr.md b/docs/versioned_docs/version-2.1.0/lr/lr.md new file mode 100644 index 0000000..f7ded6f --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lr/lr.md @@ -0,0 +1,51 @@ +--- +sidebar_position: 1 +--- + +# LR class + +A class to store the data, methods and artifacts for _Logistic Regression_. + +## Syntax + +```python +LR(settings: LRSettings, array_scores: np.ndarray, y: np.ndarray): +``` + +## Constructor parameters + +- `settings`: object of type [`LRSettings`](./lrsettings.md). Contains the settings for + the `LR` object. +- `array_scores`: `np.ndarray`, product of [`PCA` analysis](../pca/). +- `y`: `np.ndarray`, product of [`PCA` analysis](../pca/). + +## Fields + +- `settings`: object of type [`LRSettings`](./lrsettings.md). Contains the settings for + the `LR` object. +- `array_scores`: product of [`PCA` analysis](../pca/). +- `y`: product of [`PCA` analysis](../pca/). +- `model`: A `LR` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `lr(self)`: performs Logistic Regression. +- `predict(self, x_sample)`: performs LR-based classification on input data. + - *raises*: + - `RuntimeError("The LR model is not trained yet!")` if prediction is + started without training the model first; + - `raise TypeError("X data for LDA prediction must be non-empty.")` if + the data passed as argument is null. + +## Example + +```python +from chemfusekit.lr import LR + +# Initialize and train the LR class +lr = LR(settings, array_scores, y) +lr.lr() + +# Perform prediction +lr.predict(x_sample) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/lr/lrsettings.md b/docs/versioned_docs/version-2.1.0/lr/lrsettings.md new file mode 100644 index 0000000..847c002 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/lr/lrsettings.md @@ -0,0 +1,44 @@ +--- +sidebar_position: 2 +--- + +# LRSettings class + +Holds the settings for the [`LR`](./lr.md) object. + +Inherits from [`BaseSettings`](../base/basesettings.md). + +## Syntax + +```python +LRSettings(algorithm: str, output: GraphMode, test_split: bool) +``` + +## Fields and constructor parameters + +- `algorithm`: the amount of components to be used in the LDA model. Defaults to + `liblinear`. Other available options: + - `lbfgs` + - `newton-cg` + - `newton-cholesky` + - `sag` + - `saga` +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles split testing. Defaults to `False`. + +The constructor raises: +- `ValueError("This algorithm does not exist.")` if the selected `algorithm` + is not a valid option. +- `Warning("You selected test_split but it won't run because you disabled the output.")` if split tests are run with `output` disabled + +## Example + +```python +from chemfusekit.lr import LRSettings, GraphMode + +settings = LRSettings( + algorithm='newton-cg', + output=GraphMode.GRAPHIC, # graphs will be printed + test_split=True # split testing is enabled +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/pca/_category_.json b/docs/versioned_docs/version-2.1.0/pca/_category_.json new file mode 100644 index 0000000..266d36f --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/pca/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "PCA module", + "position": 3, + "link": { + "type": "generated-index", + "description": "A module for principal component analysis." + } +} diff --git a/docs/versioned_docs/version-2.1.0/pca/pca.md b/docs/versioned_docs/version-2.1.0/pca/pca.md new file mode 100644 index 0000000..1a07127 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/pca/pca.md @@ -0,0 +1,46 @@ +--- +sidebar_position: 1 +--- + +# PCA class + +A class to store the data, methods and artifacts for _Principal Component Analysis_. + +## Syntax + +```python +PCA(settings: PCASettings, data: BaseDataModel) +``` + +## Constructor parameters + +- `settings`: object of type [`PCASettings`](./pcasettings.md). Contains the settings for + the `PCA` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +## Fields + +- `fused_data`: object of type [`LLDF`](../lldf/lldf-class.md). Contains the data to be analyzed. +- `components`: Number of components for the PCA analysis. Defaults to 0. +- `pca_model`: A `PCA` model from `scikit-learn`. Defaults to `None`. +- `settings`: object of type [`PCASettings`](./pcasettings.md). Contains the settings for + the `PCA` object. + +## Methods + +- `pca(self)`: performs Principal Component Analysis +- `pca_stats(self)` produces PCA-related statistics and graphs. + +## Example + +```python +from chemfusekit.pca import PCA + +# Initialize and run the PCA class +pca = PCA(lldf.fused_data, pca_settings) +pca.pca() + +# Print the number of components and the statistics +print(pca.components) +pca.pca_stats() +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/pca/pcadatamodel.md b/docs/versioned_docs/version-2.1.0/pca/pcadatamodel.md new file mode 100644 index 0000000..31cb3cb --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/pca/pcadatamodel.md @@ -0,0 +1,25 @@ +--- +sidebar_position: 3 +--- + +# PCADataModel class + +This class models the output data from the [`PCA`](./pca.md) operation. + +It inherits from the [`BaseDataModel`](../base/basedatamodel.md). + +## Syntax + +```python +PCAModel(x_data: pd.DataFrame, x_train: pd.DataFrame, y: np.ndarray, array_scores: np.ndarray) +``` + +## Fields and constructor parameters + +The first two are `Pandas` `DataFrame` objects: +- `x_data` +- `x_train` + +The last two are `NumPy` `ndarray`s: +- `y` +- `array_scores` diff --git a/docs/versioned_docs/version-2.1.0/pca/pcasettings.md b/docs/versioned_docs/version-2.1.0/pca/pcasettings.md new file mode 100644 index 0000000..ca533ea --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/pca/pcasettings.md @@ -0,0 +1,41 @@ +--- +sidebar_position: 2 +--- + +# PCASettings class + +Holds the settings for the [`PCA`](./pca.md) object. + +## Syntax + +```python +PCASettings( + target_variance: float, + confidence_level: float, + initial_components: int, + output: GraphMode +) +``` + +## Fields and constructor parameters + +- `target_variance`: the minimum cumulative explained variance to reach in the analysis. + Defaults to 0.95. +- `confidence_level`: the confidence level for statistical tests. Defaults to 0.05. +- `initial_components`: the minimum amount of components to be used in the PCA model. + Defaults to 10. +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). + +## Example + +```python +from chemfusekit.pca import PCASettings, GraphMode + +# Initialize the settings for Principal Component Analysis +pca_settings = PCASettings( + target_variance=0.99, + confidence_level=0.05, + initial_components=10, + output=GraphMode.GRAPHIC # graphs will be printed +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/plsda/_category_.json b/docs/versioned_docs/version-2.1.0/plsda/_category_.json new file mode 100644 index 0000000..aaf0cbf --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/plsda/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "PLSDA module", + "position": 7, + "link": { + "type": "generated-index", + "description": "A module for partial least squares discriminant analysis." + } +} diff --git a/docs/versioned_docs/version-2.1.0/plsda/plsda.md b/docs/versioned_docs/version-2.1.0/plsda/plsda.md new file mode 100644 index 0000000..3287fd6 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/plsda/plsda.md @@ -0,0 +1,47 @@ +--- +sidebar_position: 1 +--- + +# PLSDA class + +A class to store the data, methods and artifacts for _Partial Least Squares Discriminant Analysis_. + +## Syntax + +```python +PLSDA(settings: PLSDASettings, data: BaseDataModel) +``` + +## Constructor parameters + +- `settings`: object of type [`PLSDASettings`](plsdasettings.md). Contains the settings for + the `PLSDA` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +## Fields + +- `settings`: object of type [`PLSDASettings`](./plsdasettings.md). Contains the settings for + the `PLSDA` object. +- `fused_data`: onject of type ['LLDFModel`](../lldf/lldfmodel.md). Contains the + artifacts from the data fusion process. +- `model`: a `PLSRegression` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `plsda(self)`: trains the Partial Least Squares Discriminant Analysis model. +- `predict(self, x_data)`: performs PLSDA prediction once the model is trained. + - *raises*: + - `RuntimeError("The PLSDA model is not trained yet!")` if the `PLSDA` model hasn't been trained yet + +## Example + +```python +from chemfusekit.knn import PLSDA + +# Initialize and run the LDA class +plsda = PLSDA(settings, lldf.fused_data) +plsda.plsda() + +# Run predictions +plsda.predict(x_data) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/plsda/plsdasettings.md b/docs/versioned_docs/version-2.1.0/plsda/plsdasettings.md new file mode 100644 index 0000000..7b547a7 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/plsda/plsdasettings.md @@ -0,0 +1,38 @@ +--- +sidebar_position: 2 +--- + +# PLSDASettings class + +Holds the settings for the [`PLSDA`](./plsda.md) object. + +Inherits from [`BaseSettings`](../base/basesettings.md). + +## Syntax + +```python +PLSDASettings(n_components: int, output: GraphMode, test_split: bool) +``` + +## Fields and constructor parameters + +- `n_components`: number of components for the PLSDA analysis. Defaults to 3. +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles the training split test phase. Defaults to `False`. Requires `output` to not be set to `GraphMode.NONE` to work. + +The constructor raises: +- `ValueError("Invalid n_components number: should be a positive integer.")` if the number of components is below 1. +- `Warning("You selected test_split but it won't run because you disabled the output.")` if `test_split` is run with `output` set to `GraphOutput.NONE` (split tests only produce graphical output, and are useless when run with disabled output). + +## Example + +```python +from chemfusekit.plsda import PLSDASettings, GraphMode + +# Initialize the settings for Partial Least Squares Discriminant Analysis +plsda_settings = PLSDASettings( + n_components=5, + output=GraphMode.GRAPHIC, # graphs will be printed + test_split=False # no split testing +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/svm/_category_.json b/docs/versioned_docs/version-2.1.0/svm/_category_.json new file mode 100644 index 0000000..f0ebda8 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/svm/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "SVM module", + "position": 5, + "link": { + "type": "generated-index", + "description": "A module for support vector machine analysis." + } +} diff --git a/docs/versioned_docs/version-2.1.0/svm/svm.md b/docs/versioned_docs/version-2.1.0/svm/svm.md new file mode 100644 index 0000000..b984ff7 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/svm/svm.md @@ -0,0 +1,49 @@ +--- +sidebar_position: 1 +--- + +# SVM class + +A class to store the data, methods and artifacts for _Support Vector Machine Analysis_. + +## Syntax + +```python +SVM(settings: SVMSettings, data: BaseDataModel) +``` + +## Constructor parameters + +- `settings`: object of type [`SVMSettings`](./svmsettings.md). Contains the settings for + the `SVM` object. +- `data`: object of type [`BaseDataModel`](../base/basedatamodel.md). Contains the data to be analyzed. + +The constructor raises: +- `ValueError("Fused data input cannot be empty.")` if the input data is null +- `valueError("Settings cannot be empty.")` if the settings are null + +## Fields + +- `fused_data`: object of type [`LLDFModel`](../lldf/lldfmodel.md). Contains the data to be analyzed. +- `settings`: object of type [`SVMSettings`](./svmsettings.md). Contains the settings for + the `PCA` object. +- `pca_model`: an `SVM` model from `scikit-learn`. Defaults to `None`. + +## Methods + +- `svm(self)`: performs Support Vector Machine analysis. + - *raises*: + - `ValueError(SVM: this type of kernel does not exist.")` if the kernel type is invalid +- `predict(self, x_data)`: performs classification based on SVM + - *raises*: + - `RuntimeError("The model hasn't been trained yet!")` if the model is null + +## Example + +```python +from chemfusekit.svm import SVM + +# Initialize and run the SVM class +svm = LDA(lldf.fused_data, settings) +svm.svm() +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/svm/svmsettings.md b/docs/versioned_docs/version-2.1.0/svm/svmsettings.md new file mode 100644 index 0000000..7ebf852 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/svm/svmsettings.md @@ -0,0 +1,43 @@ +--- +sidebar_position: 2 +--- + +# SVMSettings class + +Holds the settings for the [`SVM`](./svm.md) object. + +Inherits from [`BaseSettings`](../base/basesettings.md). + +## Syntax + +```python +SVMSettings(kernel: str, output: GraphMode, test_split: bool) +``` + +## Fields and constructor parameters + +- `kernel`: the type of kernel to use in the SVM analysis. Available options: + - `linear` + - `poly` + - `gaussian` + - `sigmoid` + Defaults to `linear`. +- `output`: toggles graph output. Defaults to [`GraphMode.NONE`](../utils/graphmode.md). +- `test_split`: toggles split testing. Defaults to `False`. + +The constructor raises: +- `ValueError("Invalid type: must be linear, poly, gaussian or sigmoid")` if the selected kernel is not one of the available +- `Warning("You selected test_split but it won't run because you disabled the output.")` if split tests are run with `output` disabled + +## Example + +```python +from chemfusekit.svm import SVMSettings, GraphMode + +# Initialize the settings for Support Vector Machine +svm_settings = SVMSettings( + type='linear', + output=GraphMode.GRAPHIC, # graphs will be printed + test_split=True # split testing is enabled +) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/tutorial.md b/docs/versioned_docs/version-2.1.0/tutorial.md new file mode 100644 index 0000000..7945b21 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/tutorial.md @@ -0,0 +1,109 @@ +--- +sidebar_position: 1 +--- + +# Tutorial + +Let's discover **Data Fusion**. + +As a simple example, we will train an LDA model and use it for classification. + +First of all, let's install the package: +```bash +pip install chemfusekit +``` + +## First step: data fusion + +We will load the `LLDFSettings` with the paths to some Excel datasheets, containing +respectively the data from a QEPAS spectrometer and a GC chromatographer. + +We will pick normalization as the preprocessing technique for the data. + +The `LLDF` class will take these settings and perform low-level data fusion on the +two Excel tables we picked. + +```python +from chemfusekit.lldf import LLDFSettings, LLDF + +# Initialize the settings for low-level data fusion +lldf_settings = LLDFSettings( + qepas_path='tests/qepas.xlsx', + qepas_sheet='Sheet1', + rt_path='tests/rt.xlsx', + rt_sheet='Sheet1', + preprocessing='snv' # normalization preprocessing; other options: savgol or both +) + +# Initialize and run low-level data fusion +lldf = LLDF(lldf_settings) +lldf.lldf() +``` + +Optionally, we can export the fused data into a new, single Excel datasheet: + +```python +# (optional) export the LLDF data to an Excel file +lldf.export_data('output_file.xlsx') +``` + +## Second step: PCA + +A run of Principal Component Analysis (`PCA`) will help us pick the right number +of components for the subsequent `LDA` analysis step. + +As in the previous case, we will set it up with the help of the `PCASettings` class. + +```python +from chemfusekit.pca import PCASettings, PCA + +# Initialize the settings for Principal Component Analysis +pca_settings = PCASettings( + target_variance=0.99, # the minimum acceptable level of cumulative explained covariance + confidence_level=0.05, # the desired level of confidence + initial_components=10, # the initial amount of components for the iterative analysis + output=GraphMode.GRAPHIC # graphs will be printed +) + +# Initialize and run the PCA class +pca = PCA(lldf.fused_data, pca_settings) +pca.pca() + +# Print the number of components and the statistics +print(pca.components) +pca.pca_stats() +``` + +## Third step: LDA training + +In this step we will set up the `LDASettings` and then run the `LDA` analysis with one less +component than what we figured out from the `PCA` analysis of the previous step. + +```python +from chemfusekit.lda import LDASettings, LDA + +settings = LDASettings( + components=(pca.components - 1), # one less component than the number determined by PCA + output=GraphMode.GRAPHIC, # graphs will be printed + test_split=True # Split testing is enabled +) + +# Initialize and run the LDA class +lda = LDA(lldf.fused_data, settings) +lda.lda() +``` + +## Fourth step: prediction + +We will pick a random sample from the dataset and see whether the trained `LDA` model +can identify it correctly. + +```python +# Let's pick a random sample from the dataset and see if it gets recognized correctly: +x_data_sample = lldf.fused_data.x_train.iloc[119] # should be DMMP +x_data_sample = x_data_sample.iloc[1:].to_frame().transpose() + +# Let's run the prediction: +predictions = lda.predict(x_data_sample) +print(predictions) +``` \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/utils/_category_.json b/docs/versioned_docs/version-2.1.0/utils/_category_.json new file mode 100644 index 0000000..322950e --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "Utilities module", + "position": 8, + "link": { + "type": "generated-index", + "description": "A module containing helper functions." + } +} diff --git a/docs/versioned_docs/version-2.1.0/utils/graphmode.md b/docs/versioned_docs/version-2.1.0/utils/graphmode.md new file mode 100644 index 0000000..bdfaa0a --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/graphmode.md @@ -0,0 +1,11 @@ +--- +sidebar-position: 1 +--- + +# GraphMode enum + +The `GraphMode` enum defines three possible values that the output of other classes can take: + +- `GRAPHIC`: graphs, tables and stats will be rendered with `Plotly`, `MatPlotLib` or `Seaborn`. Best used with `Jupyter Notebook`; +- `TEXT`: output will be rendered as plain text. The best option for offline batch processing; +- `NONE`: output will be suppressed completely. \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/utils/graphoutput.md b/docs/versioned_docs/version-2.1.0/utils/graphoutput.md new file mode 100644 index 0000000..362bd7f --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/graphoutput.md @@ -0,0 +1,20 @@ +--- +sidebar-position: 2 +--- + +# `graph_output` function + +A (partially) reusable graphing function shared by different classes. Not meant for direct usage. + +## Syntax + +```python +graph_output(scores, model, name: str, mode: GraphMode) +``` + +## Parameters + +- `scores`: the scores that are output by the model fitting function +- `model`: a `scikit-learn` classification model +- `name`: a `str` representing the name of the analysis technique +- `mode`: a [`GraphMode`](./graphmode.md) enum that acts as an output selector diff --git a/docs/versioned_docs/version-2.1.0/utils/printconfusionmatrix.md b/docs/versioned_docs/version-2.1.0/utils/printconfusionmatrix.md new file mode 100644 index 0000000..826c2f2 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/printconfusionmatrix.md @@ -0,0 +1,19 @@ +--- +sidebar-position: 5 +--- + +# `print_confuson_matrix` function + +A multimodal confusion matrix and classification report printer utility. Not meant for direct usage. + +## Syntax + +```python +print_confusion_matrix(y1, y2, title: str, mode: GraphMode) +``` + +## Parameters + +- `y1` and `y2`: the true and predicted values +- `title`: a `str` representing the title for the confusion matrix and classification report +- `mode`: a [`GraphMode`](./graphmode.md) enum that acts as an output selector \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/utils/printtable.md b/docs/versioned_docs/version-2.1.0/utils/printtable.md new file mode 100644 index 0000000..a07206e --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/printtable.md @@ -0,0 +1,20 @@ +--- +sidebar-position: 3 +--- + +# `print_table` function + +A multimodal table printing utility. It can output tables as `Plotly` plots or as plain text. Not meant for direct usage. + +## Syntax + +```python +print_table(header_values, cell_values, title: str, mode: GraphMode) +``` + +## Parameters + +- `header_values`: the column titles +- `cell_values`: a row array of column arrays +- `title`: a `str` containing the title for the table +- `mode`: a [`GraphMode`](./graphmode.md) enum that acts as an output selector \ No newline at end of file diff --git a/docs/versioned_docs/version-2.1.0/utils/runsplittests.md b/docs/versioned_docs/version-2.1.0/utils/runsplittests.md new file mode 100644 index 0000000..410eb65 --- /dev/null +++ b/docs/versioned_docs/version-2.1.0/utils/runsplittests.md @@ -0,0 +1,20 @@ +--- +sidebar-position: 4 +--- + +# `run_split_tests` function + +A reusable function for split testing a generic model. Not meant for direct usage. + +## Syntax + +```python +run_split_test(x, y, model, extended=False, mode: GraphMode) +``` + +## Parameters + +- `x` and `y`: the regressor and target arrays +- `model`: a `scikit-learn` classifier +- `extended`: a `bool` that selects whether a longer split analysis will be carried out +- `mode`: a [`GraphMode`](./graphmode.md) enum that acts as an output selector diff --git a/docs/versioned_sidebars/version-2.0-sidebars.json b/docs/versioned_sidebars/version-1.2.0-sidebars.json similarity index 100% rename from docs/versioned_sidebars/version-2.0-sidebars.json rename to docs/versioned_sidebars/version-1.2.0-sidebars.json diff --git a/docs/versioned_sidebars/version-2.0.0-sidebars.json b/docs/versioned_sidebars/version-2.0.0-sidebars.json new file mode 100644 index 0000000..caea0c0 --- /dev/null +++ b/docs/versioned_sidebars/version-2.0.0-sidebars.json @@ -0,0 +1,8 @@ +{ + "tutorialSidebar": [ + { + "type": "autogenerated", + "dirName": "." + } + ] +} diff --git a/docs/versioned_sidebars/version-2.1.0-sidebars.json b/docs/versioned_sidebars/version-2.1.0-sidebars.json new file mode 100644 index 0000000..caea0c0 --- /dev/null +++ b/docs/versioned_sidebars/version-2.1.0-sidebars.json @@ -0,0 +1,8 @@ +{ + "tutorialSidebar": [ + { + "type": "autogenerated", + "dirName": "." + } + ] +} diff --git a/docs/versions.json b/docs/versions.json index 2ccba82..b619bc6 100644 --- a/docs/versions.json +++ b/docs/versions.json @@ -1,5 +1,6 @@ [ - "2.0", - "1.2", + "2.1.0", + "2.0.0", + "1.2.0", "1.1.3" ]