From 25d09ee315bc9b44f90e80c60117b71043c7e04a Mon Sep 17 00:00:00 2001
From: Andreas Hellerschmied <--local>
Date: Fri, 30 Dec 2022 09:45:41 +0100
Subject: [PATCH] Minor changs for release 0.0.3: code cleanup, file headers,
command line help for ls2csv, etc.
---
README.md | 22 +++++++++++++++++--
lifescale/command_line/__init__.py | 18 ++++++++++++++++
lifescale/command_line/command_line.py | 29 ++++++++++++++++++++++----
lifescale/models/__init__.py | 18 ++++++++++++++++
lifescale/models/ls_data.py | 27 ++++++++++++++++++------
lifescale/scripts/__init__.py | 18 ++++++++++++++++
lifescale/scripts/ls2csv.py | 20 +++++++++++++++---
7 files changed, 137 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index e702bcb..790f669 100644
--- a/README.md
+++ b/README.md
@@ -11,8 +11,26 @@ files (where `[run-name]` is the name from the settings sheet):
* `SampleSummary_[run-name].csv`: Data from the sheet IntervalAnalysis plus sample related data from AcquisitionIntervals.
### Usage:
- * Conversion: `ls2csv -i [path and nale of xlsm file] -o [outpur directory] [-s] [-nv]`
- * Help: `ls2csv -h`
+```
+ls2csv -i [path and nale of xlsm file] -o [outpur directory] [-s] [-nv]
+
+options:
+ -h, --help show this help message and exit
+ -i INPUT_XLSM, --input-xlsm INPUT_XLSM
+ Path and name of the input xlsm file created by
+ lifescale. (default: None)
+ -o OUT_DIR, --out-dir OUT_DIR
+ Output directory for the CSV files. (default: None)
+ -nv, --not-verbose Disable command line status messages. (default: False)
+ -s, --sample-stats Calculate sample statistics of masses (median, std.
+ deviation, quartiles, interquartile range) and add
+ them to the SampleSummary output CSV file (columns:
+ Mass_median, Mass_std, Mass_q25, Mass_q75,Mass_iqr).
+ (default: False)
+ -t, --sort-masses-by-time
+ Sort data in the Masses CSV file by acquisition time.
+ (default: False)
+```
# License and copyright
diff --git a/lifescale/command_line/__init__.py b/lifescale/command_line/__init__.py
index e69de29..522bb39 100644
--- a/lifescale/command_line/__init__.py
+++ b/lifescale/command_line/__init__.py
@@ -0,0 +1,18 @@
+"""LifeScale utils command line interface module.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+:Authors:
+ Andreas Hellerschmied (heller182@gmx.at)
+"""
\ No newline at end of file
diff --git a/lifescale/command_line/command_line.py b/lifescale/command_line/command_line.py
index ea86d34..86eff8c 100644
--- a/lifescale/command_line/command_line.py
+++ b/lifescale/command_line/command_line.py
@@ -1,6 +1,19 @@
"""Command line interface of lifescale utils.
Copyright (C) 2022 Andreas Hellerschmied <heller182@gmx.at>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
from lifescale.scripts.ls2csv import ls2csv as ls2csv_main
@@ -36,19 +49,27 @@ def ls2csv():
parser.add_argument("-o", "--out-dir", type=is_dir, required=True, help="Output directory for the CSV files.")
parser.add_argument("-nv", "--not-verbose", required=False, help="Disable command line status messages.",
action='store_true')
- parser.add_argument("-s", "--sample-stats", required=False, help="Calculate sample statistics (mean, median, IQR, "
- "StDev.) and add it to the output CSV files.",
+ parser.add_argument("-s", "--sample-stats", required=False, help="Calculate sample statistics of masses (median, "
+ "std. deviation, quartiles, interquartile range) "
+ "and add them to the "
+ "SampleSummary output CSV file (columns: "
+ "Mass_median, Mass_std, Mass_q25, Mass_q75,"
+ "Mass_iqr).",
action='store_true')
- # parser.add_argument("--out-dir", type=is_dir, required=False,
- # help="path to output directory", default=OUT_PATH)
+ parser.add_argument("-t", "--sort-masses-by-time", required=False, help="Sort data in the Masses CSV file by "
+ "acquisition time.",
+ action='store_true')
+
args = parser.parse_args()
verbose = not args.not_verbose
return ls2csv_main(xlsm_filename=args.input_xlsm,
output_dir=args.out_dir,
sample_stats=args.sample_stats,
+ sort_by_time=args.sort_masses_by_time,
verbose=verbose)
if __name__ == '__main__':
+ """Main function for debugging and testing."""
ls2csv()
diff --git a/lifescale/models/__init__.py b/lifescale/models/__init__.py
index e69de29..c91b869 100644
--- a/lifescale/models/__init__.py
+++ b/lifescale/models/__init__.py
@@ -0,0 +1,18 @@
+"""LifeScale utils objects module.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+:Authors:
+ Andreas Hellerschmied (heller182@gmx.at)
+"""
\ No newline at end of file
diff --git a/lifescale/models/ls_data.py b/lifescale/models/ls_data.py
index 73c1cb0..f60d18a 100644
--- a/lifescale/models/ls_data.py
+++ b/lifescale/models/ls_data.py
@@ -132,7 +132,7 @@ class LSData:
input_xlsm_filename : str
Filename and path of the xlsm file written by LifeScale.
verbose : bool, optional (default = `True`)
- If `True`. status messages are written to the command line.
+ If `True`, status messages are written to the command line.
Returns
-------
@@ -140,7 +140,7 @@ class LSData:
Contains all LS output data loaded from the given xlsm file.
"""
- REQUIRED_XLSM_SHEET_NAMES = [
+ REQUIRED_XLSM_SHEET_NAMES = [ # Raise an exception if they are not present in the input xlsm file.
'AcquisitionIntervals',
'IntervalAnalysis',
'PanelData',
@@ -412,8 +412,24 @@ class LSData:
df_masses=df_masses,
)
- def export_csv_files(self, output_filepath, verbose=True, sort_by_time=False):
- """Write CSV files to output directory"""
+ def export_csv_files(self, output_filepath, sort_by_time=False, verbose=True):
+ """Write CSV files to output directory
+
+ Parameters
+ ----------
+ output_filepath : str
+ Path to the output directory.
+ sort_by_time : bool, optional (default=`False`)
+ Sort data in the Masses CSV file by the observation time.
+ verbose : bool, optional (default = `True`)
+ If `True`, status messages are written to the command line.
+
+ Returns
+ -------
+ :py:obj:`.LSData`
+ Contains all LS output data loaded from the given xlsm file.
+
+ """
if verbose:
print('Write output')
@@ -453,7 +469,6 @@ class LSData:
# TODO: Output format (number of digits)
# TODO: Select columns for output (settable as parameter + default settings for each csv file)
- # TODO: Optionally order data series by time (parameter)?!
def calc_sample_statistics(self, verbose=True):
"""Calculate statistical values for each sample and add it to the self.df_interval_analysis."""
@@ -534,4 +549,4 @@ if __name__ == '__main__':
ls_data = LSData.from_xlsm_file(input_xlsm_filename=xlsm_filename)
ls_data.export_csv_files(output_directory)
- print('test')
+ print('End')
diff --git a/lifescale/scripts/__init__.py b/lifescale/scripts/__init__.py
index e69de29..5ba464a 100644
--- a/lifescale/scripts/__init__.py
+++ b/lifescale/scripts/__init__.py
@@ -0,0 +1,18 @@
+"""LifeScale utils scripts module.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+:Authors:
+ Andreas Hellerschmied (heller182@gmx.at)
+"""
\ No newline at end of file
diff --git a/lifescale/scripts/ls2csv.py b/lifescale/scripts/ls2csv.py
index 92f4bd1..55c902b 100644
--- a/lifescale/scripts/ls2csv.py
+++ b/lifescale/scripts/ls2csv.py
@@ -1,13 +1,27 @@
"""Conversion program from xlsm to csv.
-Copyright (C) 2022 Andreas Hellerschmied <heller182@gmx.at>"""
+Copyright (C) 2022 Andreas Hellerschmied <heller182@gmx.at>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
from lifescale.models.ls_data import LSData
-def ls2csv(xlsm_filename, output_dir, sample_stats=True, verbose=True):
+def ls2csv(xlsm_filename, output_dir, sample_stats=True, sort_by_time=False, verbose=True):
"""Convert lifescale output file (xlsm) to csv files."""
ls_data = LSData.from_xlsm_file(input_xlsm_filename=xlsm_filename, verbose=verbose)
if sample_stats:
ls_data.calc_sample_statistics(verbose=verbose)
- ls_data.export_csv_files(output_dir, verbose=verbose)
+ ls_data.export_csv_files(output_dir, sort_by_time=sort_by_time, verbose=verbose)
--
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