update user docs

Author: backmari

docs/images/binning_options_button_apply_to_all_runs.png

@@ -6,10 +6,16 @@ Binning a Reduced Workspace in QuickNXS
 Overview
 --------
 
-Binning is an essential process in reflectivity reduction within QuickNXS, organizing raw data into manageable intervals for accurate analysis.
-There are two steps during which binning occurs:
-1. An initial time-of-flight binning step to process the raw event data, which is later converted into Q bins (mandatory).
-2. A final Q rebinning is optionally available for user who want their reflectivity output in specific Q binning.
+Binning is an essential process in reflectivity reduction within QuickNXS,
+organizing raw data into manageable intervals for accurate analysis.
+There are two types of binning: time-of-flight binning and Q binning.
+
+An initial **time-of-flight binning** step processes the raw event data from the
+sample run and direct beam run to allow for normalization. This step is
+mandatory.
+
+There is an optional **Q binning** step, which happens when the reflectivity
+data is converted to Q-space.
 
 This guide explains the available binning options in QuickNXS and how to configure them.
 
@@ -40,97 +46,66 @@ The following options allow users to fine-tune binning behavior:
       **Entering the Bin Width**
 
 
-**Final Rebin** (Checkbox, Per-Run)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+**Binning Type** (Multi-select, Per-Run)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-   - **What It Does:** Controls whether the final reduced workspace (converted to Q-space) undergoes additional rebinning.
+   - **What It Does:** Controls the binning of the final reduced workspace (converted to Q-space).
    - **How It Works:**
+      - There are three options for `Q binning`, which happens when the reflectivity
+        data is converted to Q-space:
 
-     - When enabled, rebinning is performed using `Q Steps`, in units of 1/Å:
-
-       - If **positive**, bins are evenly spaced.
-       - If **negative**, bins are spaced logarithmically using a geometric progression.
+         1. `None`: the counts from the pixels in the region-of-interest are summed
+            in pixel-time space and then converted to Q. No additional binning.
+         2. `Normal binning`: the counts from the pixels in the region-of-interest
+            are summed in pixel-time space and then converted to Q. Finally, the
+            resulting counts vs Q data is binned according to the configured Q
+            binning.
+         3. `Constant-Q binning`: the data is first converted to Q and then summed
+            according to the configured Q binning to produce counts vs Q.
 
-     - This option is **only available** if `Constant-Q Binning` is **disabled**.
-     - If `Constant-Q Binning` is enabled, it **takes priority** over `Final Rebin`.
-     - If `Final Rebin` is enabled for a run, the `Q Steps` values can be viewed and updated in the reduction data table under the `Q-Steps` column.
-     - The button `Apply final rebin to runs` applies final rebin with the same `Q Steps` value for all runs in the active reduction data table.
+      - For `Normal binning` and `Constant-Q binning`, rebinning is performed
+        using `Q Steps`, in units of 1/Å:
 
-   - **How to Use It:** Check this box if you want to apply final rebinning for the active run, or use the button to apply final rebin for all runs.
+         - If **positive**, bins are evenly spaced.
+         - If **negative**, bins are spaced logarithmically using a geometric progression.
 
-   .. figure::
-      ../images/final_rebin_button.png
-      :alt: Apply Final Rebin to All Runs
-
-      **Apply Final Rebin to All Runs in the Active Reduction Data Table**
+   - **How to Use It:** Select the binning type either in the reduction table
+     or (for the active run) in the left-hand side panel `Reflectivity
+     Extraction (Per Run)`.
 
-   .. figure::
-      ../images/final_rebin_per_run.png
-      :alt: Final Rebin Per-Run Checkbox
-
-      **Enabling Final Rebin Per-Run**
-
-
-**Constant-Q Binning** (Checkbox, Applied Globally)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-   - **What It Does:** uses the position of each pixel and the specified TOF binning to sum counts directly in Q bins. This differs from the traditional reflectivity calculation, which assumes that all counts in a TOF bin has the same Q value regardless of where they landed on the detector.
-   - **How It Works:**
-
-     - When enabled, `Final Rebin` is not performed.
-     - Enabling Constant-Q binning changes the way R(q) is calculated.
-     - `Q Steps` is used to determine binning:
-
-       - If **positive**, bins are evenly spaced.
-       - If **negative**, bins are spaced logarithmically using a geometric progression.
-
-     - This setting is **global** and cannot be adjusted per-run.
-
-   - **How to Use It:** Check this box if you want to maintain constant-Q binning. Ensure `Q Steps` is set appropriately for either linear or logarithmic binning.
-
-   .. figure::
-      ../images/constant_q_binning.png
-      :alt: Constant-Q Binning
-
-      **Enabling Constant-Q Binning**
-
-**Q Steps** (Numeric Input, Per-Run or Global)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+**Q Steps** (Numeric Input, Per-Run)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
    - **Constraints:** Must be a floating point value between -0.1 and 0.1 units of 1/Å.
-   - **What It Does:** Defines the bin width for the final rebinning in Q-space.
+   - **What It Does:** Defines the bin width for the rebinning in Q-space.
    - **How It Works:**
 
-     - `Q Steps` is used in both `Final Rebin` and `Constant-Q Binning`.
-     - When `Final Rebin` is enabled, `Q Steps` sets the bin width for the final rebinning.
-     - When `Constant-Q Binning` is enabled, `Q Steps` determines whether binning follows a **linear** or **logarithmic** scale.
+     - `Q Steps` is used for both `Normal` and `Constant-Q` binning.
+     - It controls the resolution of the final reduced workspace.
 
-       - It controls the resolution of the final reduced workspace.
        - If `Q Steps` is **positive**, linear binning is applied with evenly spaced bins.
        - If `Q Steps` is **negative**, logarithmic binning is applied, where bin edges follow a geometric progression.
 
-   - **How to Use It:** Enter a numeric value to specify the bin width for Q-space rebinning. Use negative values for logarithmic binning.
+   - **How to Use It:** Enter a numeric value to specify the bin width for
+     Q-space binning. Use negative values for logarithmic binning.
 
    .. figure::
-      ../images/q_steps_global0.png
-      :alt: Q Steps Global
+      ../images/binning_options_per_run.png
+      :alt: Binning Options for the Active Run
 
+      **Changing Binning Options for the Active Run**
 
    .. figure::
-      ../images/q_steps_global1.png
-      :alt: Q Steps Global
+      ../images/binning_options_reduction_table.png
+      :alt: Binning Options in the Reduction Table
 
-      **Setting Q Steps Globally disables the Q-Steps column in the reduction table**
-
-   .. figure::
-      ../images/q_steps_per_run0.png
-      :alt: Q Steps Per-Run
+      **Changing Binning Options in the Reduction Table**
 
    .. figure::
-      ../images/q_steps_per_run1.png
-      :alt: Q Steps Per-Run
+      ../images/binning_options_button_apply_to_all_runs.png
+      :alt: Apply the Same Binning Options to All Runs
 
-      **Setting Q Steps Per-Run adds the value to the Q-Steps column in the reduction table**
+      **Apply the Same Binning Options to All Runs in the Reduction Table**
 
 Binning Workflow
 ----------------
@@ -144,12 +119,16 @@ To apply binning settings effectively, follow these steps:
    - If TOF min is ≤ 0, `Bin Width` will also be used as the TOF minimum.
    - The direct beam workspace is automatically rebinned to match this setting.
 
-1. **Apply Final Binning (Optional):**
+1. **Apply Q Binning (Optional):**
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-   - If `Constant-Q Binning` is **enabled**, it takes priority over `Final Rebin`.
-   - If `Constant-Q Binning` is **disabled** and additional Q-space binning is required, check `Final Rebin` and specify a `Q Steps` value.
-   - If `Final Rebin` is enabled **per-run**, the `Q Steps` values can be viewed and updated in the reduction data table under the `Q-Steps` column.
-   - If using `Constant-Q Binning`, ensure `Q Steps` is appropriately set for linear or logarithmic binning.
+   - Select the binning type and Q steps for each run, either in the reduction
+     table or in the panel `Reflectivity Extraction (Per Run)`. Alternatively,
+     to set the same binning type and Q steps for all runs in the reduction
+     table, use the button `Apply to all runs` under `Reflectivity Extraction
+     (Global)`.
+   - The reflectivity plot is updated automatically when updating binning
+     options.
 
-By adjusting these options, users can customize their reflectivity reduction workflow to achieve the desired data resolution and accuracy.
+By adjusting these options, users can customize their reflectivity reduction
+workflow to achieve the desired data resolution and accuracy.