From b7658bf28a2d625c3e636bdd71310f01336dfed4 Mon Sep 17 00:00:00 2001
From: Manuel Guth <manuel.guth@cern.ch>
Date: Thu, 30 Jan 2020 12:45:37 +0000
Subject: [PATCH 1/2] adding tests for GetScales function
---
umami/configs/DL1r_Variables.yaml | 24 ++++++-------
umami/preprocessing.py | 40 ++++++++-------------
umami/preprocessing_tools/Configuration.py | 3 +-
umami/preprocessing_tools/Resampling.py | 6 ++--
umami/preprocessing_tools/__init__.py | 2 +-
umami/tests/test_preprocessing_tools.py | 41 +++++++++++++++++++++-
6 files changed, 72 insertions(+), 44 deletions(-)
diff --git a/umami/configs/DL1r_Variables.yaml b/umami/configs/DL1r_Variables.yaml
index 18a829a1c..536aa35b5 100644
--- a/umami/configs/DL1r_Variables.yaml
+++ b/umami/configs/DL1r_Variables.yaml
@@ -50,15 +50,15 @@ spectator_variables:
- DL1r_pb
- DL1r_pu
- custom_defaults_vars:
- JetFitter_energyFraction: 0
- JetFitter_significance3d: 0
- JetFitter_nVTX: -1
- JetFitter_nSingleTracks: -1
- JetFitter_nTracksAtVtx: -1
- JetFitter_N2Tpair: -1
- SV1_N2Tpair: -1
- SV1_NGTinSvx: -1
- SV1_efracsvx: 0
- secondaryVtx_nTrks: 0
- secondaryVtx_EFrac: 0
+custom_defaults_vars:
+ JetFitter_energyFraction: 0
+ JetFitter_significance3d: 0
+ JetFitter_nVTX: -1
+ JetFitter_nSingleTracks: -1
+ JetFitter_nTracksAtVtx: -1
+ JetFitter_N2Tpair: -1
+ SV1_N2Tpair: -1
+ SV1_NGTinSvx: -1
+ SV1_efracsvx: 0
+ secondaryVtx_nTrks: 0
+ secondaryVtx_EFrac: 0
diff --git a/umami/preprocessing.py b/umami/preprocessing.py
index 7f5719671..258157bc5 100644
--- a/umami/preprocessing.py
+++ b/umami/preprocessing.py
@@ -45,9 +45,8 @@ def GetParser():
return args
-def RunUndersampling():
+def RunUndersampling(args):
"""Applies required cuts to the samples and applies the downsampling."""
- args = GetParser()
config = upt.Configuration(args.config_file)
N_list = upt.GetNJetsPerIteration(config)
@@ -157,28 +156,16 @@ def RunUndersampling():
# python Preprocessing.py --no_writing --downsampled --only_scale
# --dummy_weights --input_file ${INPUTFILE} -f params_MC16D-2019-VRjets -o ""
-def GetScaleDict():
- args = GetParser()
+def GetScaleDict(args):
config = upt.Configuration(args.config_file)
- # TODO: find good way to get file names
+ # TODO: find good way to get file names, breaks if no iterations
input_file = config.GetFileName(iteration=1, option='downsampled')
infile_all = h5py.File(input_file, 'r')
- # TODO: add properly Variable config
- config.variable_config = "/home/fr/fr_fr/fr_mg1150/workspace/btagging/"\
- "umami/umami/configs/DL1r_Variables.yaml"
- # TODO: check if dictfile already exists in proper way
- # dict_dir = "./"
- # dict_file = "test.json"
- input_file = "test.h5"
- print('Preprocessing', input_file)
-
- with open(config.variable_config, "r") as conf:
+ with open(args.var_dict, "r") as conf:
variable_config = yaml.load(conf, Loader=yaml_loader)
- var_list = [variable_config["label"], "category"]
- var_list += variable_config["train_variables"]
- var_list += variable_config["spectator_variables"]
+ var_list = variable_config["train_variables"]
bjets = pd.DataFrame(infile_all['bjets'][:][var_list])
cjets = pd.DataFrame(infile_all['cjets'][:][var_list])
@@ -198,20 +185,21 @@ def GetScaleDict():
# no scaling and shifting is applied to the check variables
scale_dict.append(upt.dict_in(var, 0., 1., None))
else:
- dict_entry = upt.Get_Shift_Scale(
+ dict_entry = upt.GetScales(
vec=X[var].values,
- w=X['weight'].values, varname=var,
+ # TODO: implement weights
+ w=np.ones(len(X)), varname=var,
custom_defaults_vars=variable_config["custom_defaults_vars"])
scale_dict.append(upt.dict_in(*dict_entry))
-
+
# save scale/shift dictionary to json file
- scale_name = '%s/%s.json' % (args.dict_dir, args.dict_file)
- with open(scale_name, 'w') as outfile:
- json.dump(scale_dict, outfile, indent=4)
- print("saved scale dictionary as", scale_name)
+ # scale_name = '%s/%s.json' % (args.dict_dir, args.dict_file)
+ # with open(scale_name, 'w') as outfile:
+ # json.dump(scale_dict, outfile, indent=4)
+ # print("saved scale dictionary as", scale_name)
if __name__ == '__main__':
args = GetParser()
# RunDownsampling()
- # GetScaleDict()
+ GetScaleDict(args)
diff --git a/umami/preprocessing_tools/Configuration.py b/umami/preprocessing_tools/Configuration.py
index bce5d026f..b8d30e77d 100644
--- a/umami/preprocessing_tools/Configuration.py
+++ b/umami/preprocessing_tools/Configuration.py
@@ -52,7 +52,7 @@ class Configuration(object):
setattr(self, elem, self.default_config[elem])
def GetFileName(self, iteration=None, option=None):
- if option is None:
+ if option is None and iteration is None:
return self.outfile_name
out_file = self.outfile_name
idx = out_file.index(".h5")
@@ -63,6 +63,5 @@ class Configuration(object):
inserttxt = f"-{option}-file-{iteration:.0f}"\
f"_{self.iterations:.0f}"
- print(inserttxt)
out_file = out_file[:idx] + inserttxt + out_file[idx:]
return out_file
diff --git a/umami/preprocessing_tools/Resampling.py b/umami/preprocessing_tools/Resampling.py
index 143c0918e..40efaaa04 100644
--- a/umami/preprocessing_tools/Resampling.py
+++ b/umami/preprocessing_tools/Resampling.py
@@ -85,8 +85,10 @@ def GetNJetsPerIteration(config):
return N_list
-def Get_Shift_Scale(vec, w, varname, custom_defaults_vars):
+def GetScales(vec, w, varname, custom_defaults_vars):
"""Calculates the weighted average and std for vector vec and weight w."""
+ if np.sum(w) == 0:
+ raise ValueError("Sum of weights has to be >0.")
# find NaN values
nans = np.isnan(vec)
# check if variable has predefined default value
@@ -101,7 +103,7 @@ def Get_Shift_Scale(vec, w, varname, custom_defaults_vars):
vec[nans] = default
average = np.ma.average(vec, weights=w)
std = np.sqrt(np.average((vec - average) ** 2, weights=w))
- return [varname, average, std, default]
+ return varname, average, std, default
def dict_in(varname, average, std, default):
diff --git a/umami/preprocessing_tools/__init__.py b/umami/preprocessing_tools/__init__.py
index 79cee7511..78f675b0b 100644
--- a/umami/preprocessing_tools/__init__.py
+++ b/umami/preprocessing_tools/__init__.py
@@ -1,4 +1,4 @@
# flake8: noqa
-from umami.preprocessing_tools.Resampling import UnderSampling, GetNJetsPerIteration, Get_Shift_Scale
+from umami.preprocessing_tools.Resampling import UnderSampling, GetNJetsPerIteration, GetScales, dict_in
from umami.preprocessing_tools.Configuration import Configuration
from umami.preprocessing_tools.Cuts import GetCuts
diff --git a/umami/tests/test_preprocessing_tools.py b/umami/tests/test_preprocessing_tools.py
index 7f21946d2..1c621d489 100644
--- a/umami/tests/test_preprocessing_tools.py
+++ b/umami/tests/test_preprocessing_tools.py
@@ -3,7 +3,7 @@ import numpy as np
import pandas as pd
import os
from umami.preprocessing_tools import UnderSampling, Configuration
-from umami.preprocessing_tools import GetNJetsPerIteration, GetCuts
+from umami.preprocessing_tools import GetNJetsPerIteration, GetCuts, GetScales
class UnderSamplingTestCase(unittest.TestCase):
@@ -92,6 +92,11 @@ class ConfigurationTestCase(unittest.TestCase):
out_file = config.GetFileName(option="test")
self.assertIn("test", out_file)
+ def test_GetFileName_no_iterations_no_input(self):
+ config = Configuration(self.config_file)
+ out_file = config.GetFileName()
+ self.assertEqual(config.outfile_name, out_file)
+
class GetNJetsPerIterationTestCase(unittest.TestCase):
"""
@@ -227,3 +232,37 @@ class PreprocessingTestCuts(unittest.TestCase):
cut_result = np.ones(len(jets))
np.put(cut_result, indices_to_remove, 0)
self.assertTrue(np.array_equal(cut_result, np.array([1, 0, 0])))
+
+
+class GetScalesTestCase(unittest.TestCase):
+ """
+ Test the implementation of the GetScales class.
+ """
+
+ def setUp(self):
+ self.arr_0 = np.zeros(500)
+ self.arr_1 = np.ones(500)
+
+ def test_ZeroCase(self):
+ varname, average, std, default = GetScales(
+ self.arr_0, self.arr_1, "zeros", {})
+ self.assertEqual(average, 0)
+ self.assertEqual(std, 0)
+ self.assertEqual(default, 0)
+
+ def test_ReturnVarname(self):
+ varname, _, _, _ = GetScales(self.arr_0, self.arr_1, "zeros", {})
+ self.assertEqual(varname, "zeros")
+
+ def test_WeightZero(self):
+ with self.assertRaises(ValueError):
+ varname, average, std, default = GetScales(
+ self.arr_1, self.arr_0, "zeros", {})
+
+ def test_OneCase(self):
+ varname, average, std, default = GetScales(
+ self.arr_1, self.arr_1, "ones", {})
+ self.assertEqual(average, 1)
+ self.assertEqual(std, 0)
+ self.assertEqual(default, 1)
+
--
GitLab
From 7e61a0b487ba888d482af38aea31eec2d7b28073 Mon Sep 17 00:00:00 2001
From: Manuel Guth <manuel.guth@cern.ch>
Date: Mon, 3 Feb 2020 11:28:27 +0000
Subject: [PATCH 2/2] switching to slim docker images and correcting linter
errors
---
.gitlab-ci.yml | 4 ++--
umami/preprocessing.py | 4 ++--
umami/tests/test_preprocessing.py | 23 ++++++++++-------------
umami/tests/test_preprocessing_tools.py | 1 -
4 files changed, 14 insertions(+), 18 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b4a6ef254..e2840c7cb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,14 +4,14 @@ stages:
unittest:
stage: test
- image: python:3.7
+ image: python:3.7-slim
script:
- pip install -r requirements.txt
- pytest ./umami/tests/ -v
linter:
stage: test
- image: python:3.7
+ image: python:3.7-slim
allow_failure: true
script:
- pip install flake8
diff --git a/umami/preprocessing.py b/umami/preprocessing.py
index 258157bc5..7eb88d45a 100644
--- a/umami/preprocessing.py
+++ b/umami/preprocessing.py
@@ -6,7 +6,7 @@ import pandas as pd
import argparse
import yaml
from umami.tools import yaml_loader
-import json
+# import json
def GetParser():
@@ -191,7 +191,7 @@ def GetScaleDict(args):
w=np.ones(len(X)), varname=var,
custom_defaults_vars=variable_config["custom_defaults_vars"])
scale_dict.append(upt.dict_in(*dict_entry))
-
+
# save scale/shift dictionary to json file
# scale_name = '%s/%s.json' % (args.dict_dir, args.dict_file)
# with open(scale_name, 'w') as outfile:
diff --git a/umami/tests/test_preprocessing.py b/umami/tests/test_preprocessing.py
index 1758f1e9a..00ba72bad 100644
--- a/umami/tests/test_preprocessing.py
+++ b/umami/tests/test_preprocessing.py
@@ -28,18 +28,15 @@ class PreprocessingTestParser(unittest.TestCase):
parser = GetParser()
self.assertEqual(parser.config_file, self.config_file)
self.assertFalse(parser.tracks)
- # self.assertIsNone(parser.cut_config_file)
-# @mock.patch('argparse.ArgumentParser.parse_args',
-# return_value=argparse.Namespace(config_file=config_file,
-# tracks=True))
-# def test_ParserTracks(self, mock_args):
-# self.parser = GetParser()
-# self.assertTrue(self.parser.tracks)
-# @mock.patch('argparse.ArgumentParser.parse_args',
-# return_value=argparse.Namespace(config_file=config_file,
-# undersampling=True))
-# def test_ParserTracks(self, mock_args):
-# self.parser = GetParser()
-# self.assertTrue(self.parser.tracks)
+class PreprocessingTestGetScaleDict(unittest.TestCase):
+ """
+ Test the implementation of the GetScaleDict function.
+ """
+ config_file = os.path.join(os.path.dirname(__file__),
+ "test_preprocess_config.yaml")
+
+ def setUp(self):
+ self.config_file = os.path.join(os.path.dirname(__file__),
+ "test_preprocess_config.yaml")
diff --git a/umami/tests/test_preprocessing_tools.py b/umami/tests/test_preprocessing_tools.py
index 1c621d489..aa0c76b65 100644
--- a/umami/tests/test_preprocessing_tools.py
+++ b/umami/tests/test_preprocessing_tools.py
@@ -265,4 +265,3 @@ class GetScalesTestCase(unittest.TestCase):
self.assertEqual(average, 1)
self.assertEqual(std, 0)
self.assertEqual(default, 1)
-
--
GitLab