From d244f0649b7afe4c6e53454da9159c6c81202be5 Mon Sep 17 00:00:00 2001
From: "Oh, Sungchan" <oh231@purdue.edu>
Date: Thu, 27 Jun 2024 16:20:22 -0400
Subject: [PATCH] Update DataGuide_AAPF_HSI.md

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 DataGuide_AAPF_HSI.md | 59 ++++++++++++++++++++++++++++++++++++++++++-
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-wefwef
+# DataGuide-AAPF-HSI
+
+This document details the file system organization and navigation procedures for accessing both unprocessed hyperspectral imaging (HSI) data and the derived phenotypic measurements of the plants captured by the [Ag Alumni Seed Phenotyping Facility (AAPF)](https://ag.purdue.edu/aapf/).
+
+- Raw Scanned Data: This folder structure houses individual scans (.hdr, .md5, .raw, .tiff) for each measurement.
+- Interim Data Product: This data contains data used for quality control procedures and images representing various vegetation indices.
+- Masterfile (.xlsx): This file contains a compilation of spreadsheets and a guide document explaining the data contents.
+
+
+### File system structure
+
+
+#### Raw Scanned Data
+
+Directories are named using a convention that incorporates both experiment number and treatment. Example: 407_WL, 407_WW, 401_20-1, 401_20-2, 401_80
+
+#### Interim Data Product
+
+
+The interim data product consists of three primary components:
+- Masterfile (`Hyperspectral_data_AAPF_experiment_{Experiment_No}.xlsx`): This file stores the derived phenotypic measurements of the plants and a guide document.
+- HSI Data Processing Quality Control Data (`quality_control`): This directory contains information for quality assessment of the HSI data processing pipeline. It includes summaries of header information for plants, white and dark reference, a detailed record of the processing procedures employed, and animated gif files used to check coregistration quality between visible and near infrared (VNIR) and shortwave infrared (SWIR) data.
+
+
+- Compressed Vegetation Index Images (`{Vegetation_Index_Type}_{ROI filter}.zip: This section houses compressed image files for various types of vegetation indices calculated from the HSI data (ROI: region of interest).
+
+
+
+Animated gif files are included to check the coregistration quality between VNIR and SWIR data per each scan.
+
+Co-registration quality between VNIR and SWIR data for each scan is visually assessed using animated GIFs
+
+- Example:
+
+    401
+    ├── Hyperspectral_data_AAPF_experiment_401.xlsx (masterfile)
+    ├── quality_control
+    │   ├── header_summary_plants.csv
+    │   ├── header_summary_ref.csv
+    │   ├── HSI_R_2401761_240514080207482_VNIR-SIDE-DAT_401_20-1_240514080219626.gif
+    │   ├── HSI_R_2401761_240514080207482_VNIR-TOP-DAT_401_20-1_24051408022152.gif
+    │   ├── HSI_R_2401761_24061408172718_VNIR-SIDE-DAT_401_20-1_240614081746352.gif
+
+
+
+└── VI_images
+
+
+The data includes RGB and fluorescence images of plants along with derived morphological measurements and phenotypic information. Here's an example breakdown:
+
+
+
+Parent directory
+Experiment_{Experiment_Nubmer}
+Example: Experiment_394
+Subdirectories
+{Parent_directory}/{Experiment_Number}_{Treatment}
+Example: Experiment_394/394_SandSoybeanHigh