Updated manuals

Author: marinerhemant

manuals/FF_Analysis.md

@@ -1,4 +1,9 @@
-**MIDAS FF-HEDM Interactive Viewer: User Manual**
+# MIDAS FF-HEDM Interactive Viewer: User Manual
+
+**Version:** 7.0  
+**Contact:** [email protected]
+
+---
 
 **1\. Introduction**
 
@@ -173,3 +178,16 @@ These plots display the data after the filters from the middle section have been
 - **Inspect Raw Data:** In the **"Filtered Spots 2D"** plot, find a spot of interest (perhaps one with very high strain) and click on it.
 - **Verify the Spot:** The **"Image Data"** plot will now show the 3D volume of the raw detector intensity around that spot. This helps confirm that it is a genuine, strong diffraction peak.
 - **Repeat:** Select a new grain or adjust the filters to continue your exploration.
+
+---
+
+## See Also
+
+- [FF_Analysis.md](FF_Analysis.md) — Standard FF-HEDM analysis (produces Grains.csv and SpotMatrix.csv)
+- [PF_Analysis.md](PF_Analysis.md) — Scanning/pencil-beam FF-HEDM analysis
+- [ForwardSimulationManual.md](ForwardSimulationManual.md) — Forward simulation for validation
+- [FF_autocalibrate.md](FF_autocalibrate.md) — Geometry calibration
+
+---
+
+If you encounter any issues or have questions, please open an issue on this repository.

manuals/FF_Interactive_Plotting.md

@@ -132,4 +132,17 @@ python /path/to/AutoCalibrateZarr.py \
     -   Data for ring overlays.
     -   Strain vs. 2-theta plots for each iteration.
     -   The final converged strain data and results dataframe.
--   **`calibrant_screen_out.csv`**: The raw text output from the last run of the `CalibrantOMP` binary. Useful for debugging backend issues.
+-   **`calibrant_screen_out.csv`**: The raw text output from the last run of the `CalibrantOMP` binary. Useful for debugging backend issues.
+
+---
+
+## See Also
+
+- [FF_Analysis.md](FF_Analysis.md) — Standard FF-HEDM analysis using calibrated geometry
+- [PF_Analysis.md](PF_Analysis.md) — Scanning/pencil-beam FF-HEDM analysis
+- [FF_dual_datasets.md](FF_dual_datasets.md) — Dual-dataset FF-HEDM analysis
+- [ForwardSimulationManual.md](ForwardSimulationManual.md) — Forward simulation for validation
+
+---
+
+If you encounter any issues or have questions, please open an issue on this repository.

manuals/FF_autocalibrate.md

@@ -9,7 +9,7 @@
 
 `ff_dual_datasets.py` is a specialized and powerful script within the MIDAS suite designed for the combined analysis of **two separate but related far-field HEDM datasets**. Its primary purpose is to process two datasets independently through the initial stages, spatially map them into a common reference frame, and then perform a single, unified indexing and refinement on the combined data.
 
-This script is ideal for scenarios such_ as:
+This script is ideal for scenarios such as:
 -   Analyzing a sample **before and after** an in-situ experiment (e.g., heating or mechanical loading).
 -   Combining two **overlapping scans** to create a larger, contiguous map.
 -   Correlating datasets collected under slightly different experimental conditions.
@@ -155,4 +155,17 @@ The script generates two initial analysis directories within the main `-resultFo
 
 -   **Mapping Fails (`MapDatasets` error):** The most common issue is incorrect offsets. Double-check the signs and values of your `-offset*` arguments. Small errors in offsets can cause the algorithm to fail to find corresponding volumes. Check `dataset_1_analysis/output/map_err.txt` for details.
 -   **Pre-processing Fails:** If one of the initial stages fails, treat it as a standard `ff_MIDAS.py` failure. Check the `output` directory of the corresponding dataset (e.g., `dataset_2_analysis/output/`) to debug issues with peak finding, data conversion, etc.
--   **Poor Indexing Results:** If the final indexing yields few grains, it could be a sign of poor alignment during the mapping stage. This can happen if the offsets are not precise enough, leading to a "blurry" or inconsistent combined dataset.
+-   **Poor Indexing Results:** If the final indexing yields few grains, it could be a sign of poor alignment during the mapping stage. This can happen if the offsets are not precise enough, leading to a "blurry" or inconsistent combined dataset.
+
+---
+
+## See Also
+
+- [FF_Analysis.md](FF_Analysis.md) — Standard single-dataset FF-HEDM analysis
+- [FF_autocalibrate.md](FF_autocalibrate.md) — Geometry calibration
+- [FF_Interactive_Plotting.md](FF_Interactive_Plotting.md) — Visualizing FF-HEDM results
+- [ForwardSimulationManual.md](ForwardSimulationManual.md) — Forward simulation for validation
+
+---
+
+If you encounter any issues or have questions, please open an issue on this repository.

manuals/FF_dual_datasets.md

@@ -1,5 +1,10 @@
 # User Manual: `ForwardSimulationCompressed`
 
+**Version:** 7.0  
+**Contact:** [email protected]
+
+---
+
 ## 1. Program Overview
 
 `ForwardSimulationCompressed` is a high-performance command-line tool for simulating far-field High Energy Diffraction Microscopy (FF-HEDM) experiments. It takes a description of a crystalline sample (grain orientations, positions, and strains) and experimental geometry as input, and produces simulated detector images as output.
@@ -165,4 +170,12 @@ The primary output of the simulation is one or more ZIP files, one for each scan
 
 To read this data, you can use Python libraries such as `zarr`.
 
+---
+
+## See Also
+
+- [FF_Analysis.md](FF_Analysis.md) — Standard FF-HEDM analysis (produces Grains.csv used as input here)
+- [FF_Interactive_Plotting.md](FF_Interactive_Plotting.md) — Visualizing FF-HEDM results and simulated data
+- [FF_autocalibrate.md](FF_autocalibrate.md) — Geometry calibration from calibrant rings
+
 ---