diff --git a/report_pre_thesis/.gitignore b/report_pre_thesis/.gitignore index 378eac25..48912d24 100644 --- a/report_pre_thesis/.gitignore +++ b/report_pre_thesis/.gitignore @@ -1 +1,2 @@ build +node_modules \ No newline at end of file diff --git a/report_pre_thesis/README.md b/report_pre_thesis/README.md new file mode 100644 index 00000000..1f8a6117 --- /dev/null +++ b/report_pre_thesis/README.md @@ -0,0 +1,19 @@ +# P9 Project: Report Pre-Thesis + +This is a technical report acting as the 'pre-thesis' for our thesis. It represents our work during the 9th semester, which will be followed by the actual thesis in the 10th semester. + +## Pipeline diagram + +To get a better understanding of the current pipeline used for ChemCam calibrations, we have created a diagram of the pipeline. + +Any edits to the pipeline should be reflected in `pipeline.mmd` using [mermaid.js](http://mermaid.js.org) syntax. + +To 'build' the pipeline, run the following command in the terminal: + +```bash +# pnpm install # - if you haven't already. Need the mermaid-cli package. +pnpm run pipeline +``` + +This will generate a file called `pipeline.png` in the `src/images` folder. The pipeline is shown below: +![ChemCam calibration pipeline](src/images/pipeline.png) diff --git a/report_pre_thesis/package.json b/report_pre_thesis/package.json new file mode 100644 index 00000000..e89c7e27 --- /dev/null +++ b/report_pre_thesis/package.json @@ -0,0 +1,9 @@ +{ + "name": "report_pre_thesis", + "scripts": { + "pipeline": "mmdc -i pipeline.mmd -o src/images/pipeline.png -t neutral -b transparent" + }, + "dependencies": { + "@mermaid-js/mermaid-cli": "^10.4.0" + } +} diff --git a/report_pre_thesis/pipeline.mmd b/report_pre_thesis/pipeline.mmd new file mode 100644 index 00000000..cdbff3a1 --- /dev/null +++ b/report_pre_thesis/pipeline.mmd @@ -0,0 +1,44 @@ +flowchart TD + subgraph DP["Data Preprocessing"] + BS[Background subtraction] --> + WO["Denoise via undecimated wavelet transformation"] --> + WC["Apply wavelength calibration"] --> + CER["Continuum removal"] -->|"Reduced Data Record (RDR)"| IRF["Apply Instrumental Response Function (IRF)"] + end + + db[(LIBS Data)] -->|"Experimental data record (EDR)"| DP + + DP -->|"Cleaned, calibrated spectra (CCS)"| C + + subgraph C["Calibration"] + Input --> NOSM["`Normalize + (Norm 1 or Norm 3)`"] --> F + F[Full Model] --> |"Initial Estimate"| H[Submodel Selection] + + SM["Submodel (Low, Mid, High)"] + BR["`Overlap range of submodels + (Low-Mid; Mid-High)`"] + + H -.->|In submodel range| SM + H -.-|Within overlap range| BR + + BR --> BO["`Blend + (*Linear weighted sum*)`"] + + SM -->|Model output| J + BO -->|Blended output| J + + Input --> WE["Weigh by inverse IRF"] --> NOI["`Normalize + (Norm 1 or Norm 3)`"] --> I + + + + I["`ICA with Joint Approximate Diagonalization of Eigenmatrices (JADE)`"] + I -->|Components & Mixing matrix| J + + + J["`Combine PLS & ICA + (_weigted average_)`"] + end + + C --> K["Multivariate Oxide Composition (MOC) Derivation"] diff --git a/report_pre_thesis/pnpm-lock.yaml b/report_pre_thesis/pnpm-lock.yaml new file mode 100644 index 00000000..025510b0 --- /dev/null +++ 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