X-Git-Url: https://git.friedersdorff.com/?a=blobdiff_plain;f=slides.rst;h=acd4a56c8e25ab9aa85f5a9d1ab17f5c5c9cbb95;hb=HEAD;hp=61080cbbe316263d5f7e713243f2c08f53836a84;hpb=e192a90c23e38e0dfb01214f379f4ce4300d98f9;p=max%2Fct_plotting.git

diff --git a/slides.rst b/slides.rst
index 61080cb..acd4a56 100644
--- a/slides.rst
+++ b/slides.rst
@@ -6,18 +6,42 @@ I am not a biologist, please stop me and correct me if I say silly things.
 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
 ---------------------
 
@@ -38,15 +62,15 @@ Spine fitting
   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
@@ -69,7 +93,9 @@ Break at Minimum Kernel Density Estimation (KDE)
 * 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
 
@@ -86,15 +112,36 @@ Break at Minimum Kernel Density Estimation (KDE)
 * 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::