Pod Width
---------
+.. image:: plot_bar_pod_widths.png
+ :width: 9cm
+
Sphericity
----------
+.. image:: plot_bar_sphericities_of_seeds.png
+ :width: 9cm
+
Volume
------
+.. image:: plot_bar_volumes_of_seeds.png
+ :width: 9cm
+
Surface Area
------------
+.. image:: plot_bar_surface_area_of_seeds.png
+ :width: 9cm
+
Correlations
------------
+.. image:: plot_correlations.png
+ :width: 8cm
+
+.. image:: plot_number_of_seeds_vs_mean_volume_of_seeds.png
+ :width: 9cm
+
+.. image:: plot_length_of_pod_vs_mean_volume_of_seeds.png
+ :width: 9cm
+
+.. image:: plot_length_of_pod_vs_number_of_seeds.png
+ :width: 9cm
+
Filtering false seeds
---------------------
the beak to the z coordinate of the point
.. image:: fitting_debug.svg
- :target: fitting_debug.gif
- :width: 1.25cm
+ :target: https://git.friedersdorff.com/max/ct_plotting/raw/master/fitting_debug.gif
+ :width: 1.22cm
-Distinguishing between beak tip and Real Seeds™
------------------------------------------------
+Classify beak tip and Real Seeds™
+---------------------------------
Failed approaches:
-##################
+
1. Assert that seeds must not be implausible - Removed insufficiently many seeds
* Too close to the ends of the pod
* Beak has no Real Seeds™ and low density
* Expect a gap in real z of detected seeds
+
.. image:: plot_real_zs_genotype_unfiltered.png
+ :width: 11cm
.. raw:: pdf
* Profit
.. image:: plot_real_zs_genotype_filtered.png
- :width: 12cm
+ :width: 11cm
.. image:: plot_real_zs_genotype_unfiltered.png
- :width: 12cm
+ :width: 11cm
Beak and Silique length
-----------------------
Use the seed with lowest real z to mark the boundary of beak and silique:
-TODO: insert silique length and beak length graphs
+.. image:: plot_bar_silique_lengths.png
+.. image:: plot_bar_beak_lengths.png
+
+Resources
+---------
+
+`Git Repository`_
+
+`This Presentation`_
+
+`Numpy`_
+
+`Matplotlib`_
+
+`Seaborne`_
+
+.. _Git Repository: https://github.com/NPPC-UK/ct_scanner_plotting
+.. _This Presentation: https://git.friedersdorff.com/max/ct_plotting.git
+.. _Numpy: https://www.numpy.org/
+.. _Matplotlib: https://matplotlib.org/
+.. _Seaborne: https://seaborn.pydata.org/
+.. target-notes::