minor changes in README.md and scripts

README.md

+<img align="right" width="300" src="./docs/_static/logo_SyConn.png"><br/>
 [![Documentation Status](https://readthedocs.org/projects/syconn/badge/?version=latest)](https://syconn.readthedocs.io/en/latest/?badge=latest)
 [![pipeline status](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/badges/master/pipeline.svg)](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/commits/master)
 [![coverage report](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/badges/master/coverage.svg)](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/commits/master)
 [![pylint status](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/-/jobs/artifacts/master/raw/pylint/pylint.svg?job=pylint)](https://gitlab.mpcdf.mpg.de/pschuber/SyConn/-/jobs/artifacts/master/raw/pylint/pylint.log?job=pylint)
 
-<img align="right" width="300"
-src="./docs/_static/logo_SyConn.png"><br/>
-
-
 SyConn
 ------
 Refactored version of SyConn for automated synaptic connectivity inference based on dense EM segmentation data. For the first version

scripts/dataset_specific/start_j0251_gce.py

@@ -27,7 +27,7 @@ if __name__ == '__main__':
     assert test_point_models or test_view_models
     experiment_name = 'j0251'
     scale = np.array([10, 10, 25])
-    number_of_nodes = 8
+    number_of_nodes = 24
     node_states = nodestates_slurm()
     node_state = next(iter(node_states.values()))
     exclude_nodes = []
@@ -40,8 +40,8 @@ if __name__ == '__main__':
     mem_per_node = node_state['memory']
     ngpus_per_node = 2  # node_state currently does not contain the number of gpus for 'gres' resource
     shape_j0251 = np.array([27119, 27350, 15494])
-    # *9 for ~3 TVx, *11 for 5.7, *7 for 1.4, *5.5 for 0.7, *4.5 for 0.4
-    cube_size = (np.array([2048, 2048, 1024]) * 4.5).astype(np.int)
+    # 10.5* for 4.9, *9 for 3.13, *7.5 for 1.81, *6 for 0.927, *4.5 for 0.391, *3 for 0.115 TVx
+    cube_size = (np.array([2048, 2048, 1024]) * 3).astype(np.int)
     # all for 10 TVx
     cube_offset = ((shape_j0251 - cube_size) // 2).astype(np.int)
     cube_of_interest_bb = np.array([cube_offset, cube_offset + cube_size], dtype=np.int)

scripts/misc/timings.py

@@ -195,10 +195,14 @@ def get_timing_plots(base_dir):
             log_reg.info(f'\n{res.summary()}\n\n')
             x_fit = np.linspace(np.min(x), np.max(x), 1000)
             y_fit = res.params[1] * x_fit + res.params[0]
-            plt.plot(x_fit, y_fit, color=palette[step])
+            # plt.plot(x_fit, y_fit, color=palette[step])
+        plt.yscale('log')
+        plt.xticks(np.arange(8, 28, step=4))
+        axes.spines['right'].set_visible(False)
+        axes.spines['top'].set_visible(False)
         axes.legend(*axes.get_legend_handles_labels(), bbox_to_anchor=(1.05, 1),
                     loc='upper left', borderaxespad=0.)
-        axes.set_ylabel('time [h]')
+        axes.set_ylabel('time [h] (log scale)')
         axes.set_xlabel('no. compute nodes [1]')
         plt.subplots_adjust(right=0.75)
         plt.savefig(base_dir + '/timing_allsteps_regplot_diff_nodes.png')
@@ -229,10 +233,14 @@ def get_timing_plots(base_dir):
             log_reg.info(f'\n{res.summary()}\n\n')
             x_fit = np.linspace(np.min(x), np.max(x), 1000)
             y_fit = res.params[1] * x_fit + res.params[0]
-            plt.plot(x_fit, y_fit, color=palette[step])
+            # plt.plot(x_fit, y_fit, color=palette[step])
+        plt.yscale('log')
+        plt.xticks(np.arange(8, 28, step=4))
+        axes.spines['right'].set_visible(False)
+        axes.spines['top'].set_visible(False)
         axes.legend(*axes.get_legend_handles_labels(), bbox_to_anchor=(1.05, 1),
                     loc='upper left', borderaxespad=0.)
-        axes.set_ylabel('time [h]')
+        axes.set_ylabel('time [h] (log scale)')
         axes.set_xlabel('no. compute nodes [1]')
         plt.subplots_adjust(right=0.75)
         plt.savefig(base_dir + '/time_allsteps_regplot_diff_nodes_wo_views.png')
@@ -314,9 +322,12 @@ def get_timing_plots(base_dir):
             x_fit = np.linspace(np.min(x), np.max(x), 1000)
             y_fit = res.params[1] * x_fit + res.params[0]
             plt.plot(x_fit, y_fit, color=palette[step])
+        plt.yscale('log')
+        axes.spines['right'].set_visible(False)
+        axes.spines['top'].set_visible(False)
         axes.legend(*axes.get_legend_handles_labels(), bbox_to_anchor=(1.05, 1),
                     loc='upper left', borderaxespad=0.)
-        axes.set_ylabel('time [h]')
+        axes.set_ylabel('time [h] (log scale)')
         axes.set_xlabel('size [GVx]')
         plt.subplots_adjust(right=0.75)
         plt.savefig(base_dir + '/timing_allsteps_regplot.png')
@@ -369,9 +380,12 @@ def get_timing_plots(base_dir):
             x_fit = np.linspace(np.min(x), np.max(x), 1000)
             y_fit = res.params[1] * x_fit + res.params[0]
             plt.plot(x_fit, y_fit, color=palette[step])
+        plt.yscale('log')
+        axes.spines['right'].set_visible(False)
+        axes.spines['top'].set_visible(False)
         axes.legend(*axes.get_legend_handles_labels(), bbox_to_anchor=(1.05, 1),
                     loc='upper left', borderaxespad=0.)
-        axes.set_ylabel('time [h]')
+        axes.set_ylabel('time [h] (log scale)')
         axes.set_xlabel('size [GVx]')
         plt.subplots_adjust(right=0.75)
         plt.savefig(base_dir + '/timing_allsteps_regplot_wo_views.png')
@@ -379,7 +393,6 @@ def get_timing_plots(base_dir):
 
 
 if __name__ == '__main__':
-    # get_timing_plots('/mnt/example_runs/')
-    # get_speed_plots('/mnt/example_runs/')
-
     get_timing_plots('/mnt/example_runs/nodes_vs_time/')
+    # get_timing_plots('/mnt/example_runs/vol_vs_time/')
+    # get_speed_plots('/mnt/example_runs/vol_vs_time')