Commit 6c1d934c authored by Philipp Schubert's avatar Philipp Schubert
Browse files

minor changes in README.md and scripts

parent 32bb0f20
Pipeline #87186 passed with stage
in 2 minutes and 9 seconds
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<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
......
......@@ -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)
......
......@@ -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')
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