From b976e848dc9293ac031ecf948999e5ae3ef0e579 Mon Sep 17 00:00:00 2001
From: hanste <s185790@student.dtu.dk>
Date: Sun, 24 Oct 2021 14:56:55 +0200
Subject: [PATCH] Added files from local to remote
---
run.py | 119 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 119 insertions(+)
create mode 100644 run.py
diff --git a/run.py b/run.py
new file mode 100644
index 0000000..847c1c1
--- /dev/null
+++ b/run.py
@@ -0,0 +1,119 @@
+import os
+import re
+import warnings
+from collections import defaultdict
+
+import numpy as np
+import matplotlib.pyplot as plt
+from tqdm import tqdm
+
+from measure import measure_cumulative_volume, measure_cumulative_points
+
+def parse_params(path):
+ with open(os.path.join(path, 'params.txt')) as f:
+ lines = f.readlines()
+
+ coords = []
+ thickness = []
+
+ for line in lines:
+ if 'origin' in line:
+ coords = [float(x) for x in re.findall('-?\d+\.?[0-9]*', line)]
+ if 'thickness' in line:
+ thickness = [float(x) for x in re.findall('-?\d+\.?[0-9]*', line)]
+
+ if len(coords) != 3:
+ print(f"found {len(coords)} coordinates when looking for 'origin' in params.txt")
+ if len(thickness) != 1:
+ print(f"found {len(coords)} coordinates when looking for 'origin' in params.txt")
+
+ thickness = thickness[0]
+
+ return coords, thickness
+
+def load_contours(path):
+ contour_dir = os.path.join(path, 'domain_contours')
+ file_fnames = os.listdir(contour_dir)
+ z_values = [float(file_fname[2:-4]) for file_fname in file_fnames]
+ z_values, file_fnames = zip(*sorted(zip(z_values, file_fnames)))
+ contours = []
+
+ for file_fname, z in zip(file_fnames, z_values):
+ X = np.loadtxt(os.path.join(contour_dir, file_fname))
+ Xp = np.pad(X, ((0,1), (0,0)), mode='wrap')
+ contours.append((z, X))
+
+ return contours
+
+
+def load_points(path):
+ point_dirs = [os.path.join(path, path_name) for path_name in os.listdir(path) if path_name.startswith('points_marker_')]
+ marker_names = [dir_name.split('points_marker_')[-1] for dir_name in point_dirs]
+
+ points = defaultdict(list)
+ for point_dir, marker_name in zip(point_dirs, marker_names):
+ file_fnames = os.listdir(point_dir)
+ z_values = [float(file_fname[2:-4]) for file_fname in file_fnames]
+ z_values, file_fnames = zip(*sorted(zip(z_values, file_fnames)))
+ for file_fname, z in zip(file_fnames, z_values):
+ X = np.loadtxt(os.path.join(point_dir, file_fname))
+ points[marker_name].append((z, X))
+
+ return points
+
+def write_csv(path, R, dP, dV):
+
+ intdP = dP[1:] - dP[:-1]
+ intdV = dV[1:] - dV[:-1]
+
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore")
+ Dens = dP / dV
+ intDens = intdP / intdV
+
+ with open(path, 'w') as f:
+ f.write(','.join(['Cummulative Reading','','','','','Interval Reading\n']))
+ f.write(','.join(['Distance','Point Counts','Volume (mu^3)','Density (n/mu^3)','','Interval start (mu)',
+ 'Interval end (mu)','Point Counts (n)','Volume (mu^3)','Density (n/mu^3)\n']))
+ for i0,i1,a,b,c,d,e,v in zip(R[:-1], R[1:], dP, dV, Dens, intdP, intdV, intDens):
+ f.write(f'{i0},{a},{b},{c},,{i0},{i1},{d},{e},{v}\n')
+
+def run(base_dir):
+
+ R = np.arange(0, 3001, 125)
+
+ output_dir = 'output'
+ os.makedirs(output_dir, exist_ok=True)
+
+ for experiment in tqdm(os.listdir(base_dir), desc='experiment'):
+ for reading in os.listdir(os.path.join(base_dir, experiment)):
+ #if reading != '7566':
+ # continue
+ data_dir = os.path.join(base_dir, experiment, reading)
+ origin, thickness = parse_params(data_dir)
+
+ contours = sorted(load_contours(data_dir))
+ points = load_points(data_dir)
+ for marker in points.keys():
+ all_points = sorted(points[marker])
+ dV = []
+ dP = []
+ for sec_contour, sec_points in zip(contours, all_points):
+ if sec_contour[0] != sec_points[0]:
+ raise ValueError('z-coordinate misalignment, does points and contour have corresponding z-value')
+ z, P = sec_contour
+ dV.append(measure_cumulative_volume(z, P, thickness, origin, R))
+ z, X = sec_points
+ dP.append(measure_cumulative_points(z, X, thickness, origin, R))
+
+ dP = np.sum(dP, axis=0)
+ dV = np.sum(dV, axis=0)
+
+ fname = f'{experiment}_{reading}_{marker}.csv'
+ path = os.path.join(output_dir, fname)
+
+ write_csv(path, R, dP, dV)
+
+if __name__ == '__main__':
+ base_dir = 'data'
+ run(base_dir)
\ No newline at end of file
--
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