From 366b4fb016682ad0da5bafb739dc76914567d9e3 Mon Sep 17 00:00:00 2001
From: Stefan Reck <stefan.reck@fau.de>
Date: Fri, 16 Apr 2021 15:28:19 +0200
Subject: [PATCH] move remaining commands to unified parser
---
orcasong/parser.py | 4 ++++
orcasong/plotting/plot_binstats.py | 18 ++++++++++++++++++
orcasong/tools/concatenate.py | 1 +
orcasong/tools/make_data_split.py | 20 +++++++++++++++++++-
orcasong/tools/postproc.py | 1 +
orcasong/tools/shuffle2.py | 1 +
setup.py | 2 +-
7 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/orcasong/parser.py b/orcasong/parser.py
index 69eecb5..df64427 100644
--- a/orcasong/parser.py
+++ b/orcasong/parser.py
@@ -7,6 +7,8 @@ from orcasong.tools.concatenate import concatenate
from orcasong.tools.postproc import postproc_file
from orcasong.tools.shuffle2 import h5shuffle2
import orcasong.from_toml as from_toml
+import orcasong.plotting.plot_binstats as plot_binstats
+import orcasong.tools.make_data_split as make_data_split
def _add_parser_concatenate(subparsers):
@@ -124,6 +126,8 @@ def main():
_add_parser_concatenate(subparsers)
_add_parser_h5shuffle(subparsers)
_add_parser_h5shuffle2(subparsers)
+ plot_binstats.add_parser(subparsers)
+ make_data_split.add_parser(subparsers)
_add_parser_version(subparsers)
kwargs = vars(parser.parse_args())
diff --git a/orcasong/plotting/plot_binstats.py b/orcasong/plotting/plot_binstats.py
index be2c8e5..e27fb7e 100644
--- a/orcasong/plotting/plot_binstats.py
+++ b/orcasong/plotting/plot_binstats.py
@@ -218,6 +218,9 @@ def get_all_h5_files():
def main():
+ # TODO deprecated
+ warnings.warn(
+ "plot_binstats is deprecated and has been renamed to orcasong plot_binstats")
parser = argparse.ArgumentParser(
description='Generate a plot with statistics of the binning. '
'Can only be used on files generated with the FileBinner when '
@@ -232,5 +235,20 @@ def main():
plot_hist_of_files(**vars(parser.parse_args()))
+def add_parser(subparsers):
+ parser = subparsers.add_parser(
+ "plot_binstats",
+ description='Generate a plot with statistics of the binning. '
+ 'Can only be used on files generated with the FileBinner when '
+ 'add_bin_stats was set to true (default). ')
+ parser.add_argument(
+ '--save_as', type=str, default="bin_stats_plot.pdf",
+ help='Filename of the plot. Default: bin_stats_plot.pdf.')
+ parser.add_argument(
+ 'files', type=str, nargs='*', default=None,
+ help='File(s) to plot. Default: Plot for all h5 files in current dir.')
+ parser.set_defaults(func=plot_hist_of_files)
+
+
if __name__ == "__main__":
main()
diff --git a/orcasong/tools/concatenate.py b/orcasong/tools/concatenate.py
index 0a86218..51c3a8d 100644
--- a/orcasong/tools/concatenate.py
+++ b/orcasong/tools/concatenate.py
@@ -324,6 +324,7 @@ def concatenate(file, outfile="concatenated.h5", no_used_files=False, skip_error
def main():
+ # TODO deprecated
warnings.warn("concatenate is deprecated and has been renamed to orcasong concatenate")
parser = argparse.ArgumentParser(
description='Concatenate many small h5 files to a single large one '
diff --git a/orcasong/tools/make_data_split.py b/orcasong/tools/make_data_split.py
index 8379862..d5f3dc7 100644
--- a/orcasong/tools/make_data_split.py
+++ b/orcasong/tools/make_data_split.py
@@ -5,6 +5,7 @@
__author__ = "Michael Moser, Daniel Guderian"
import os
+import warnings
import toml
import argparse
import h5py
@@ -13,6 +14,8 @@ import numpy as np
def get_parser():
+ # TODO deprecated
+ warnings.warn("make_data_split is deprecated and has been renamed to orcasong make_data_split")
parser = argparse.ArgumentParser(
description="Create datasets based on the run_id's."
"Use the config to add input folder and set the ranges."
@@ -26,6 +29,20 @@ def get_parser():
return parser
+def add_parser(subparsers):
+ parser = subparsers.add_parser(
+ "make_data_split",
+ description="Create datasets based on the run_id's."
+ "Use the config to add input folder and set the ranges."
+ "Outputs a list in an txt file that can be used to "
+ "concatenate the files specfied"
+ )
+ parser.add_argument(
+ "config", type=str, help="See example config for detailed information"
+ )
+ parser.set_defaults(func=make_split)
+
+
def get_all_ip_group_keys(cfg):
"""
Gets the keys of all input groups in the config dict.
@@ -418,9 +435,10 @@ def main():
# load the config
parser = get_parser()
parsed_args = parser.parse_args()
+ make_split(parsed_args.config)
- config_file = parsed_args.config
+def make_split(config_file):
# decode config
cfg = toml.load(config_file)
cfg["toml_filename"] = config_file
diff --git a/orcasong/tools/postproc.py b/orcasong/tools/postproc.py
index acd3c38..45cc320 100644
--- a/orcasong/tools/postproc.py
+++ b/orcasong/tools/postproc.py
@@ -117,6 +117,7 @@ def get_filepath_output(input_file, shuffle=True, event_skipper=None):
def h5shuffle():
+ # TODO deprecated
warnings.warn("h5shuffle is deprecated and has been renamed to orcasong h5shuffle")
parser = argparse.ArgumentParser(description='Shuffle an h5 file using km3pipe.')
parser.add_argument('input_file', type=str, help='File to shuffle.')
diff --git a/orcasong/tools/shuffle2.py b/orcasong/tools/shuffle2.py
index 11083e1..0fcdaa7 100644
--- a/orcasong/tools/shuffle2.py
+++ b/orcasong/tools/shuffle2.py
@@ -337,6 +337,7 @@ def slicify(fancy_indices):
def run_parser():
+ # TODO deprecated
warnings.warn("h5shuffle2 is deprecated and has been renamed to orcasong h5shuffle2")
parser = argparse.ArgumentParser(
description="Shuffle datasets in a h5file that have the same length. "
diff --git a/setup.py b/setup.py
index 281186f..0ad200d 100644
--- a/setup.py
+++ b/setup.py
@@ -28,9 +28,9 @@ setup(
entry_points={'console_scripts': [
'orcasong=orcasong.parser:main',
+ # TODO all deprecated:
'make_dsplit=orcasong.tools.make_data_split:main',
'plot_binstats=orcasong.plotting.plot_binstats:main',
- # deprecated:
'concatenate=orcasong.tools.concatenate:main',
'h5shuffle=orcasong.tools.postproc:h5shuffle',
'h5shuffle2=orcasong.tools.shuffle2:run_parser',
--
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