Update documentation for refining workflow

README.md

@@ -49,6 +49,7 @@ The easiest way to get started is to drop a folder (typically a folder from with
 - `E`, to enable edge coloring (by default, if using this in refinement GUI mode, points with a confidence lower than 0.6 are marked
 in red)
 - `F`, to toggle between animal and body part color scheme.
+- `V`, to toggle visibility of the selected layer.
 - `backspace` to delete a point.
 - Check the box "display text" to show the label names on the canvas.
 - To move to another folder, be sure to save (Ctrl+S), then delete the layers, and re-drag/drop the next folder.
@@ -61,6 +62,7 @@ Only when saving segmentation masks does a save file dialog pop up to name the d
 keypoint annotations are otherwise automatically saved in the corresponding folder as `CollectedData_<ScorerName>.h5`.
 - As a reminder, DLC will only use the H5 file; so be sure if you open already labeled images you save/overwrite the H5.
 - Note, before saving a layer, make sure the points layer is selected. If the user clicked on the image(s) layer first, does `Save As`, then closes the window, any labeling work during that session will be lost!
+- Modifying and then saving points in a `machinelabels...` layer will add to or overwrite the existing `CollectedData` layer and will **not** save to the `machinelabels` file. 
 
 
 ### Video frame extraction and prediction refinement
@@ -106,13 +108,50 @@ Suggested workflows, depending on the image folder contents:
 3. **Refining labels** – the image folder contains a `machinelabels-iter<#>.h5` file.
 
     The process is analog to *2*.
+    Open *napari* and open an image folder.
+    If the video was originally labeled, *and* had outliers extracted it will contain a `CollectedData_<ScorerName>.h5` file and a `machinelabels-iter<#>.h5` file. In this case, select the `machinelabels` layer in the GUI, and type `e` to show edges. Red indicates likelihood < 0.6. As you navigate through frames, images with labels with edges will need to be refined (moved, deleted, etc). Images with labels without edges will be on the `CollectedData` (previous manual annotations) layer and shouldn't need refining. However, you can switch to that layer and fix errors. You can also right-click on the `CollectedData` layer and select `toggle visibility` to hide that layer. Select the `machinelabels` layer before saving which will append your refined annoations to `CollectedData`.
+
+    If the folder only had outliers extracted and wasn't originally labeled, it will not have a `CollectedData` layer. Work with the `machinelabels` layer selected to refine annoation positions, then save.
+
+    In this case, it is not necessary to open the DLC project's `config.yaml` file, as all necessary metadata is read from the `h5` data file.
+
+    Saving works as described in *1*.
 
 4. **Drawing segmentation masks**
 
     Drop an image folder as in *1*, manually add a *shapes layer*. Then select the *rectangle* in the layer controls (top left pane),
     and start drawing rectangles over the images. Masks and rectangle vertices are saved as described in [Save Layers](#save-layers).
     Note that masks can be reloaded and edited at a later stage by dropping the `vertices.csv` file onto the canvas.
 
+### Workflow flowchart
+
+```mermaid
+%%{init: {"flowchart": {"htmlLabels": false}} }%%
+graph TD
+  id1[What stage of labeling?]
+  id2[deeplabcut.label_frames]
+  id3[deeplabcut.refine_labels]
+  id4[Add labels to, or modify in, \n `CollectedData...` layer and save that layer]
+  id5[Modify labels in `machinelabels` layer and save \n which will create a `CollectedData...` file]
+  id6[Have you refined some labels from the most recent iteration and saved already?]
+  id7["All extracted frames are already saved in `CollectedData...`. 
+1. Hide or trash all `machinelabels` layers.
+2. Then modify in and save `CollectedData`"]
+  id8["
+1. hide or trash all `machinelabels` layers except for the most recent. 
+2. Select most recent `machinelabels` and hit `e` to show edges. 
+3. Modify only in `machinelabels` and skip frames with labels without edges shown.
+4. Save `machinelabels` layer, which will add data to `CollectedData`. 
+	- If you need to revisit this video later, ignore `machinelabels` and work only in `CollectedData`"]
+
+  id1 -->|I need to manually label new frames \n or fix my labels|id2
+  id1 ---->|I need to refine outlier frames \nfrom analyzed videos|id3
+  id2 -->id4
+  id3 -->|I only have a `machinelabels...` file|id5
+  id3 ---->|I have both `machinelabels` and `CollectedData` files|id6
+  id6 -->|yes|id7
+  id6 ---->|no, I just extracted outliers|id8
+```
 
 ### Labeling multiple image folders