Merge pull request #2 from chhoumann/pipeline

Add pipeline diagram

report_pre_thesis/.gitignore

@@ -1 +1,2 @@
 build
+node_modules

report_pre_thesis/README.md

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+# 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)

report_pre_thesis/package.json

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+{
+  "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"
+  }
+}

report_pre_thesis/pipeline.mmd

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+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"]