diff --git a/docs/_static/images/disordered_tracing/ts2_dis_metrics.png b/docs/_static/images/disordered_tracing/ts2_dis_metrics.png new file mode 100644 index 00000000000..7d12cbf9185 Binary files /dev/null and b/docs/_static/images/disordered_tracing/ts2_dis_metrics.png differ diff --git a/docs/_static/images/disordered_tracing/ts2_metrics-branch.png b/docs/_static/images/disordered_tracing/ts2_metrics-branch.png new file mode 100644 index 00000000000..28bdc0d42d9 Binary files /dev/null and b/docs/_static/images/disordered_tracing/ts2_metrics-branch.png differ diff --git a/docs/_static/images/grainstats/ts2_gs_metrics.png b/docs/_static/images/grainstats/ts2_gs_metrics.png new file mode 100644 index 00000000000..10e3d7e05a6 Binary files /dev/null and b/docs/_static/images/grainstats/ts2_gs_metrics.png differ diff --git a/docs/_static/images/nodestats/ts2_ns_metrics.png b/docs/_static/images/nodestats/ts2_ns_metrics.png new file mode 100644 index 00000000000..c4ac6bc1596 Binary files /dev/null and b/docs/_static/images/nodestats/ts2_ns_metrics.png differ diff --git a/docs/_static/images/ordered_tracing/ts2_metrics-mols.png b/docs/_static/images/ordered_tracing/ts2_metrics-mols.png new file mode 100644 index 00000000000..f035c61e140 Binary files /dev/null and b/docs/_static/images/ordered_tracing/ts2_metrics-mols.png differ diff --git a/docs/_static/images/ordered_tracing/ts2_ord_metrics.png b/docs/_static/images/ordered_tracing/ts2_ord_metrics.png new file mode 100644 index 00000000000..c4036bb174d Binary files /dev/null and b/docs/_static/images/ordered_tracing/ts2_ord_metrics.png differ diff --git a/docs/_static/images/splining/ts2_metrics-mols_1.png b/docs/_static/images/splining/ts2_metrics-mols_1.png new file mode 100644 index 00000000000..883b8e9b126 Binary files /dev/null and b/docs/_static/images/splining/ts2_metrics-mols_1.png differ diff --git a/docs/_static/images/splining/ts2_sp_metrics.png b/docs/_static/images/splining/ts2_sp_metrics.png new file mode 100644 index 00000000000..57fd38055e4 Binary files /dev/null and b/docs/_static/images/splining/ts2_sp_metrics.png differ diff --git a/docs/advanced.md b/docs/advanced.md index 2120e6da89d..014d37fca4c 100644 --- a/docs/advanced.md +++ b/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) diff --git a/docs/advanced/disordered_tracing.md b/docs/advanced/disordered_tracing.md index 63722b7147e..a99a4ad0e62 100644 --- a/docs/advanced/disordered_tracing.md +++ b/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: diff --git a/docs/advanced/grainstats.md b/docs/advanced/grainstats.md new file mode 100644 index 00000000000..ac8a18049ca --- /dev/null +++ b/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) diff --git a/docs/advanced/nodestats.md b/docs/advanced/nodestats.md index 26ea6975eaf..e9b4a072918 100644 --- a/docs/advanced/nodestats.md +++ b/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 `.topostats` file found within the `processed` folder and contains a multitude of grain and branch statistics such as: diff --git a/docs/advanced/ordered_tracing.md b/docs/advanced/ordered_tracing.md index 12f7ae89553..d8bae6584bd 100644 --- a/docs/advanced/ordered_tracing.md +++ b/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 `.topostats` file found within the `processed` folder and contains a multitude of molecule related objects such as: diff --git a/docs/advanced/splining.md b/docs/advanced/splining.md index 1a0bdc60760..92e21e93595 100644 --- a/docs/advanced/splining.md +++ b/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 `.topostats` file found within the `processed` folder and contains a multitude of molecule related objects such as: