Merge pull request #24 from flatironinstitute/iss18_notebook_plots

Iss18 notebook plots

config_files/config_plotting.yaml

@@ -0,0 +1,13 @@
+gt_metadata: path/to/metadata.csv
+
+map2map_results:
+  - path/to/map2map_results_1.pkl
+  - path/to/map2map_results_2.pkl
+
+dist2dist_results:
+  pkl_fnames:
+    - path/to/dist2dist_results_1.pkl
+    - path/to/dist2dist_results_2.pkl
+  pkl_globs:
+    - string/path/with/wildcards/and/regex/filestem*_field1[0-9].pkl
+    - string/path/with/wildcards/and/regex/filestem*_field1[0-9]_field2[0-9].pkl

src/cryo_challenge/_distribution_to_distribution/distribution_to_distribution.py

@@ -13,6 +13,13 @@
 )
 
 
+def sort_by_transport(cost):
+    m,n = cost.shape
+    _, transport = compute_wasserstein_between_distributions_from_weights_and_cost(np.ones(m) / m, np.ones(n)/n, cost)
+    indices = np.argsort((transport * np.arange(m)[...,None]).sum(0))
+    return cost[:,indices], indices, transport
+
+
 def compute_wasserstein_between_distributions_from_weights_and_cost(
     weights_a, weights_b, cost, numItermax=1000000
 ):

src/cryo_challenge/_ploting/plotting_utils.py

@@ -0,0 +1,6 @@
+import numpy as np
+
+def res_at_fsc_threshold(fscs, threshold=0.5):
+    res_fsc_half = np.argmin(fscs > threshold, axis=-1)
+    fraction_nyquist = 0.5*res_fsc_half / fscs.shape[-1]
+    return res_fsc_half, fraction_nyquist