From cf0f1fad7ccc2dbddb0c1cdc249a756365c776b8 Mon Sep 17 00:00:00 2001
From: "Oh, Sungchan" <oh231@purdue.edu>
Date: Thu, 27 Jun 2024 17:17:24 -0400
Subject: [PATCH] Update DataGuide_AAPF_HSI.md

---
 DataGuide_AAPF_HSI.md | 49 ++++++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 19 deletions(-)

diff --git a/DataGuide_AAPF_HSI.md b/DataGuide_AAPF_HSI.md
index b55984a..0fcb66d 100644
--- a/DataGuide_AAPF_HSI.md
+++ b/DataGuide_AAPF_HSI.md
@@ -25,7 +25,7 @@ This document details the file system organization and navigation procedures for
 - Parent directory
     - {Experiment_Number}_{Treatment}
     - Example: 407_WL, 407_WW, 401_20-1, 401_20-2, 401_80
-- Data Files
+- Data files
     - `Header File (.hdr)`: This file stores metadata associated with the data acquisition process. It includes information such as sensor specifications, date and time of capture, etc.
     - `MD5 File (.md5)`: This file contains a Message Digest 5 (MD5) checksum. The MD5 checksum is a unique identifier generated from the data itself and can be used to verify data integrity. Any accidental corruption during storage or transmission will result in a mismatch between the calculated MD5 checksum and the one stored in the file.
     - `Hyperspectral Datacube (.raw)`: This file stores the raw hyperspectral data. A hyperspectral datacube is a three-dimensional array where each layer represents a two-dimensional image captured at a specific wavelength band.
@@ -34,10 +34,35 @@ This document details the file system organization and navigation procedures for
 
 #### 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).
+    Example (does not contain all associated files):
+    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
+        ├── NDVI_default.zip
+        ├── NDWI_default.zip
+        ├── NLI_default.zip
+        └── NMDI_default.zip
+
+- Parent directory
+    - {Experiment_Number}
+    - Example: 401, 407
+- Subdirectories
+    - qualtiy control
+    - VI_images
+- Data files
+    - `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).
+
+
+    - `Header File (.hdr)`: This file stores metadata associated with the data acquisition process. It includes information such as sensor specifications, date and time of capture, etc.
+
 
 - Parent directory
     - {Experiment_Number}
@@ -50,20 +75,6 @@ The interim data product consists of three primary components:
     - Example: 401/VI_images
 
 
-    Example (does not contain all associated files):
-        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
-            ├── NDVI_default.zip
-            ├── NDWI_default.zip
-            ├── NLI_default.zip
-            └── NMDI_default.zip