Update DataGuide_AAPF_HSI.md

DataGuide_AAPF_HSI.md

@@ -9,29 +9,29 @@ This document details the file system organization and navigation procedures for
 
 ### File system structure
 
+#### Raw Scanned Data
 
-    #### 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
 
-    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
+    - Example (does not contain all associated files):
+    401
+    ├── HSI_R_2401856_240606084952173_SWIR-SIDE-DAT_401_80_240606085015154.hdr
+    ├── HSI_R_2401856_240606084952173_SWIR-SIDE-DAT_401_80_240606085015154.md5
+    ├── HSI_R_2401856_240606084952173_SWIR-SIDE-DAT_401_80_240606085015154.raw
+    ├── HSI_R_2401856_240606084952173_SWIR-SIDE-DAT_401_80_240606085015154.tiff
+    ├── HSI_R_2401856_240606084952173_SWIR-TOP-DAT_401_80_240606085006035.hdr
+    ├── HSI_R_2401856_240606084952173_SWIR-TOP-DAT_401_80_240606085006035.md5
+    ├── HSI_R_2401856_240606084952173_SWIR-TOP-DAT_401_80_240606085006035.raw
+    └── HSI_R_2401856_240606084952173_SWIR-TOP-DAT_401_80_240606085006035.tiff
 
-    #### Interim Data Product
+#### Interim Data Product
 
-
-    The interim data product consists of three primary components:
+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:
-
+
+    - Example (does not contain all associated files):
         401
         ├── Hyperspectral_data_AAPF_experiment_401.xlsx (masterfile)
         ├── quality_control
@@ -46,7 +46,7 @@ Co-registration quality between VNIR and SWIR data for each scan is visually ass
             ├── NLI_default.zip
             └── NMDI_default.zip
 
-The data includes RGB and fluorescence images of plants along with derived morphological measurements and phenotypic information. Here's an example breakdown:
+