more clean up

CovertLab · Jun 11, 2018 · 13eb27d · 13eb27d
1 parent 53bfafa
commit 13eb27d
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Showing 8 changed files with 20 additions and 217 deletions.
diff --git a/TODO b/TODO
diff --git a/TODO 2018-2-26.txt b/TODO 2018-2-26.txt
diff --git a/figures/figure4_fit.py b/figures/figure4_fit.py
@@ -157,25 +157,6 @@ def get_residuals_and_indexing(directory):
 	return residuals, indexing
 
 def main(input_directory, output_directory):
-	# valid = np.load(os.path.join(input_directory, 'valid.npy'))
-
-	# pars = np.load(os.path.join(input_directory, 'pars.npy'))[
-	# 	:, valid
-	# 	]
-
-	# abs_res, abs_ind = get_absolute_fit_residuals(pars)
-	# rel_res, rel_ind = get_relative_fit_residuals(pars)
-
-	# residuals = np.row_stack([abs_res, rel_res])
-	# indexing = np.concatenate([abs_ind, rel_ind])
-
-	# sorting = np.argsort(indexing)
-
-	# residuals = residuals[sorting, :]
-	# indexing = indexing[sorting]
-
-	# datatypes = indexing['datatype']
-
 	(residuals, indexing) = get_residuals_and_indexing(input_directory)
 
 	datatypes = indexing['datatype']
@@ -184,6 +165,9 @@ def main(input_directory, output_directory):
 
 	# make_clean_directory(output_directory)
 
+	if not os.path.exists(output_directory):
+		os.makedirs(output_directory)
+
 	n_unique = 0
 	n_within_2x_median = 0
 	n_within_10x_median = 0
@@ -239,5 +223,5 @@ def main(input_directory, output_directory):
 if __name__ == '__main__':
 	main(
 		os.path.join('out', 'all_scaled'),
-		'figure5'
+		'figure4'
 		)
diff --git a/figures/figure4_fit_alt.py b/figures/figure4_fit_alt.py
@@ -1,16 +1,16 @@
 
 import os
 
-import figure5
+import figures.figure4_fit
 
 inputs_and_outputs = tuple(
 	(
 		os.path.join('out', 'all_scaled_upper_sat_limits_{}'.format(penalty)),
-		os.path.join('figure5', 'saturation penalized', 'penalty_{}'.format(penalty))
+		os.path.join('figure4', 'saturation penalized', 'penalty_{}'.format(penalty))
 		)
 	for penalty in ('1e-1', '1e0', '1e1', '1e2')
 	)
 
 for input_and_output in inputs_and_outputs:
-	figure5.main(*input_and_output)
+	figures.figure4_fit.main(*input_and_output)
 	print ''
diff --git a/figures/figure5_dynamics.py b/figures/figure5_dynamics.py
@@ -294,4 +294,4 @@ def init_dg_dt(pars):
 	plt.subplot(len(sources), 2, i*2+2)
 	plot_prd(pars, i)
 
-plt.savefig('figure4.pdf')
+plt.savefig('figure5.pdf')
diff --git a/figures/figure6_predictions.py b/figures/figure6_predictions.py
@@ -10,8 +10,6 @@
 import structure
 import constants
 
-from figure5 import make_clean_directory
-
 def main(input_directory, output_directory):
 	pars = np.load(os.path.join(input_directory, 'pars.npy'))[
 		:, np.load(os.path.join(input_directory, 'valid.npy'))
@@ -83,7 +81,8 @@ def main(input_directory, output_directory):
 
 	fig = utils.residuals.plot(residuals, indexing)
 
-	# make_clean_directory(output_directory)
+	if not os.path.exists(output_directory):
+		os.makedirs(output_directory)
 
 	fig.savefig(os.path.join(output_directory, 'specific_activity.pdf'), dpi = DPI)
 

diff --git a/figures/figure6_predictions_alt.py b/figures/figure6_predictions_alt.py
@@ -1,7 +1,7 @@
 
 import os
 
-import figure6
+import figures.figure6_predictions
 
 inputs_and_outputs = tuple(
 	(
@@ -12,5 +12,5 @@
 	)
 
 for input_and_output in inputs_and_outputs:
-	figure6.main(*input_and_output)
+	figures.figure6_predictions.main(*input_and_output)
 
diff --git a/figures/figure6_shifted_distributions.py b/figures/figure6_shifted_distributions.py
@@ -8,8 +8,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-import figure5
-from ks_test import ks_test
+import figures.figure4_fit
 
 import utils.residuals
 
@@ -18,15 +17,15 @@
 if not os.path.exists(OUTPUT_DIRECTORY):
 	os.mkdir(OUTPUT_DIRECTORY)
 
-(residuals_standard, indexing_standard) = figure5.get_residuals_and_indexing(
+(residuals_standard, indexing_standard) = figures.figure4_fit.get_residuals_and_indexing(
 	os.path.join('out', 'all_scaled')
 	)
 
-(residuals_small, indexing_small) = figure5.get_residuals_and_indexing(
+(residuals_small, indexing_small) = figures.figure4_fit.get_residuals_and_indexing(
 	os.path.join('out', 'all_scaled_upper_sat_limits_1e-1')
 	)
 
-(residuals_large, indexing_large) = figure5.get_residuals_and_indexing(
+(residuals_large, indexing_large) = figures.figure4_fit.get_residuals_and_indexing(
 	os.path.join('out', 'all_scaled_upper_sat_limits_1e2')
 	)
 
@@ -61,14 +60,14 @@
 
 	fig = utils.residuals.plot(residuals[plotted], indexing[plotted])
 
-	fig.savefig(os.path.join(OUTPUT_DIRECTORY, '{}.pdf'.format(name)), dpi = figure5.DPI)
+	fig.savefig(os.path.join(OUTPUT_DIRECTORY, '{}.pdf'.format(name)), dpi = figures.figure4_fit.DPI)
 
 	plt.close(fig)
 
 with open(os.path.join(OUTPUT_DIRECTORY, 'key.txt'), 'w') as f:
 	for uni in unique_values[shifted_large]:
 		f.write(':'.join([
-			figure5.DATATYPES_ORDERED[uni['datatype']] if uni['datatype'] >= 0 else '',
-			figure5.REACTIONS_ORDERED[uni['reaction']] if uni['reaction'] >= 0 else '',
-			figure5.COMPOUNDS_ORDERED[uni['compound']] if uni['compound'] >= 0 else '',
+			figures.figure4_fit.DATATYPES_ORDERED[uni['datatype']] if uni['datatype'] >= 0 else '',
+			figures.figure4_fit.REACTIONS_ORDERED[uni['reaction']] if uni['reaction'] >= 0 else '',
+			figures.figure4_fit.COMPOUNDS_ORDERED[uni['compound']] if uni['compound'] >= 0 else '',
 			])+'\n')