Added rough grainstats summary documentation and metric images

docs/advanced.md

@@ -5,6 +5,7 @@ You can read more detailed information about the methods implemented in TopoStat
 - [Flattening](advanced/flattening.md)
 - [Grain Finding](advanced/grain_finding.md)
 - [Thresholding](advanced/thresholding.md)
+- [Grain Stats](advanced/grainstats.md)
 - [Disordered Tracing](advanced/disordered_tracing.md)
 - [Nodestats](advanced/nodestats.md)
 - [Ordered Tracing](advanced/ordered_tracing.md)

docs/advanced/disordered_tracing.md

@@ -124,6 +124,10 @@ For each grain, the following new columns are added to the `grainstats.csv` file
 | `grain_junctions`     | The number of pixels designated as junctions (>2 neighbours) in the pruned skeleton.    | `integer` |
 | `total_branch_length` | The sum of all branch lengths in the pruned skeleton.                                   | `float`   |
 
+ 
+
+![Disordered tracing grain metrics visualisation](../_static/images/disordered_tracing/ts2_dis_metrics.png)
+
 ### Disordered Segment Statistics
 
 An `all_disordered_segment_statistics.csv` file is produced for each image which measures the following metrics from
@@ -145,6 +149,10 @@ each segment in each pruned skeleton:
 | `mid-value`          | The value of a pixel halfway along the ordered branch (height), in nm.                                                     | `float`   |
 | `basename`           | The directory path containing the image.                                                                                   | `string`  |
 
+ 
+
+![Disordered tracing branch metrics visualisation](../_static/images/disordered_tracing/ts2_metrics-branch.png)
+
 ## Diagnostic Images
 
 Images produced by the `plotting.image_set: all` for this module are:

docs/advanced/grainstats.md

@@ -0,0 +1,25 @@
+# Grainstats
+
+## At a Glance - Measures Objects
+
+TopoStats automatically tries to measure the grains (objects of interest) found in the grain finding section, in your
+AFM images, and outputs them into the `all_statistics.csv` file.
+
+The metrics are briefly summarised in the table below:
+
+| Column Name                      | Description                                                                                                                                                | Data Type |
+| -------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- |
+| `center_x/y`                     | The center of the grain.                                                                                                                                   | `float`   |
+| `radius_min/max/mean/median`     | The distance from the center to each pixel on the perimeter.                                                                                               | `float`   |
+| `height_min/max/mean/median`     | The pixel values underlying the grain mask.                                                                                                                | `float`   |
+| `area`                           | The area of the pixel-wise grain mask.                                                                                                                     | `float`   |
+| `volume`                         | Volume of the pixel-wise grain mask.                                                                                                                       | `float`   |
+| `area_cartesian_bbox`            | The area of a box bounding the grain along cardinal directions.                                                                                            | `float`   |
+| `smallest_bounding_width/length` | The shortest bounding box length and perpendicular width of the grain in non-cardinal directions.                                                          | `float`   |
+| `smallest_bounding_area`         | The area of the smallest possible box bounding the grain.                                                                                                  | `float`   |
+| `aspect_ratio`                   | Ratio of the smallest bounding width to smallest bounding length.                                                                                          | `float`   |
+| `max/min_feret`                  | The largest and shortest distance of the calipers rotating the grain between calipers. See [feret diameter](https://en.wikipedia.org/wiki/Feret_diameter). | `float`   |
+
+ 
+
+![Grain Stats image table pt1](../_static/images/grainstats/ts2_gs_metrics.png)

docs/advanced/nodestats.md

@@ -124,6 +124,8 @@ For each grain, the following new columns are added to the `grainstats.csv` file
 
  
 
+![NodeStats grain metrics visualisation](../_static/images/NodeStats/ts2_ns_metrics.png)
+
 Note: Most information obtained during the NodeStats processing can be obtained from the `<image_name>.topostats` file
 found within the `processed` folder and contains a multitude of grain and branch statistics such as:
 

docs/advanced/ordered_tracing.md

@@ -138,6 +138,8 @@ For each grain, the following new columns are added to the `grainstats.csv` file
 
  
 
+![Ordered tracing grain metrics visualisation](../_static/images/ordered_tracing/ts2_ord_metrics.png)
+
 For each molecule found by the ordering algorithm(s), the following new columns are added to the `molstats.csv` file:
 
 | Column Name     | Description                                                                                                         | Data Type |
@@ -149,6 +151,8 @@ For each molecule found by the ordering algorithm(s), the following new columns
 
  
 
+![Ordered tracing molecule metrics visualisation](../_static/images/ordered_tracing/ts2_metrics-mols.png)
+
 Note: Most information obtained during the Ordered Tracing processing can be obtained from the `<image_name>.topostats`
 file found within the `processed` folder and contains a multitude of molecule related objects such as:
 

docs/advanced/splining.md

@@ -91,6 +91,8 @@ For each grain, the following new columns are added to the `grainstats.csv` file
 
  
 
+![Splined tracing molecule metrics visualisation](../_static/images/splining/ts2_sp_metrics.png)
+
 For each molecule found by the ordering algorithm(s), the following new columns are added to the `molstats.csv` file:
 
 | Column Name           | Description                                                           | Data Type |
@@ -100,6 +102,8 @@ For each molecule found by the ordering algorithm(s), the following new columns
 
  
 
+![Splined tracing molecule metrics visualisation](../_static/images/splining/ts2_metrics-mols_1.png)
+
 Note: Most information obtained during the Splining processing can be obtained from the `<image_name>.topostats` file
 found within the `processed` folder and contains a multitude of molecule related objects such as: