From 472dca50a02049587b67755bbf4b55f63c46b8fe Mon Sep 17 00:00:00 2001
From: Alice BRENON <alice.brenon@ens-lyon.fr>
Date: Fri, 5 Jan 2024 12:22:52 +0100
Subject: [PATCH] Add the ability to set the resolution from the command line
in the profile visualisation script
---
scripts/textometry/visualiseProfile.py | 34 +++++++++++++++++++-------
1 file changed, 25 insertions(+), 9 deletions(-)
diff --git a/scripts/textometry/visualiseProfile.py b/scripts/textometry/visualiseProfile.py
index 54c5ef5..47bc44a 100755
--- a/scripts/textometry/visualiseProfile.py
+++ b/scripts/textometry/visualiseProfile.py
@@ -12,9 +12,10 @@ def gate(measure):
return [1 if i >= first and i < last else 0
for i in range(1, 1 + measure['totalSize'])]
-def plotProfile(profile, outputPath):
+def plotDensity(profile, outputPath):
plot.figure(figsize=(16,13))
- ax = seaborn.lineplot(profile)
+ l = len(profile)
+ ax = seaborn.lineplot(x=[100*i/(l-1) for i in range(l)], y=profile)
ax.set_xlabel("Position")
ax.set_xlim(0, 100)
ax.set_ylim(0)
@@ -29,7 +30,7 @@ def plotProfile(profile, outputPath):
def sumProfiles(sameSizeProfiles):
return list(map(sum, zip(*sameSizeProfiles)))
-def computeProfile(measures, resolution=100):
+def computeProfile(measures, resolution):
bySize, count = {}, 0
for measure in measures:
distribution = gate(measure)
@@ -39,13 +40,28 @@ def computeProfile(measures, resolution=100):
bySize[l] = []
bySize[l].append(distribution)
resampled = map(resample(resolution), map(sumProfiles, bySize.values()))
- return [100*x/count for x in sumProfiles(list(resampled))]
+ return [resolution*x/count for x in sumProfiles(list(resampled))]
-def visualiseProfile(measures, outputPath):
- profile = computeProfile(measures)
+def visualiseProfile(measures, outputPath, resolution=100):
+ profile = computeProfile(measures, resolution)
toTSV(prepare(f"{outputPath}/profile.tsv"), profile, sortBy=None)
- plotProfile(profile, f"{outputPath}/profile.png")
+ plotDensity(profile, f"{outputPath}/profile.png")
+
+def parseArgs(args):
+ positional = []
+ kwargs = {}
+ i = 0
+ while i < len(args):
+ if args[i] == '--resolution':
+ kwargs['resolution'] = int(args[i+1])
+ i += 1
+ else:
+ positional.append(args[i])
+ i += 1
+ return positional, kwargs
if __name__ == '__main__':
- visualiseProfile([measure for _, measure in fromTSV(argv[1]).iterrows()],
- argv[2])
+ args, kwargs = parseArgs(argv[1:])
+ visualiseProfile([measure for _, measure in fromTSV(args[0]).iterrows()],
+ args[1],
+ **kwargs)
--
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